[ { "id": "Q86VI3-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "IHDLYGKVKFTAEELSNMAS", "down_seq": "LAKYGLQLPAFSKIGGILAN", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "1", "chr_pos": "156563640", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E178", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86VI3-1.162.162", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86VI3-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1482500897", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482500897", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1482500897", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482500897", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ANELSVDEAAVHAAVLAINE", "down_seq": "VERGVVEDTLAALQNPSALL", "snv": [ { "evidence": [ { "id": "rs1482500897", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482500897" }, { "id": "rs1482500897", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482500897" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEA->NET).", "chr_id": "1", "chr_pos": "156563283", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A217", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86VI3-1.201.201", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86VI3-1.233.233", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1314320250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314320250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1314320250", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314320250", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AINEAVERGVVEDTLAALQN", "down_seq": "SALLENLREPLAAVYQEMLA", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" }, { "id": "rs1314320250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314320250" }, { "id": "rs1314320250", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314320250" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NLS).", "chr_id": "1", "chr_pos": "156563234", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P233", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86VI3-1.217.217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs570977840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs570977840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs570977840", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs570977840", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs570977840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs570977840", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs570977840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs570977840", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ANTKGDQEQAMLHAVQRINK", "down_seq": "IRRRVAADTVKELMCPEAQL", "snv": [ { "evidence": [ { "id": "rs570977840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs570977840" }, { "id": "rs570977840", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs570977840" }, { "id": "rs570977840", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs570977840" }, { "id": "rs570977840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs570977840" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKA->NKT).", "chr_id": "1", "chr_pos": "156556664", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A387", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DEQRRQNVAYQYLCRLEEAK", "down_seq": "WMEACLKEELPSPVELEESL", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "156569377", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R42", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQQQQGELGQEELFVAVEML", "down_seq": "AVVLINRALEARDASGFWSS", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "156554349", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S445", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.534.534", "start_pos": 534, "end_pos": 534, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1394424706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394424706", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1394424706", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394424706", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VNAQTQEETDRVLAVSLINE", "down_seq": "LDKGSPEKTLSALLLPAAGL", "snv": [ { "evidence": [ { "id": "rs1394424706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394424706" }, { "id": "rs1394424706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394424706" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEA->NET).", "chr_id": "1", "chr_pos": "156551839", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A534", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q86VI3-1.539.539", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1299231398", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299231398", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1299231398", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299231398", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLWLEEIRQGVVRANQDTNT", "down_seq": "QRMALGVAAINQAIKEGKAA", "snv": [ { "evidence": [ { "id": "rs1299231398", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299231398" }, { "id": "rs1299231398", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299231398" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "1", "chr_pos": "156550270", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A606", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q86VI3-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q86VI3-1.619.619", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WLEEIRQGVVRANQDTNTAQ", "down_seq": "MALGVAAINQAIKEGKAAQT", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "156550263", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R608", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q86VI3-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q86VI3-1.619.619", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.619.619", "start_pos": 619, "end_pos": 619, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ANQDTNTAQRMALGVAAINQ", "down_seq": "IKEGKAAQTERVLRNPAVAL", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQA->NQS).", "chr_id": "1", "chr_pos": "156548719", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A619", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q86VI3-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q86VI3-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q86VI3-1.636.636", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.636.636", "start_pos": 636, "end_pos": 636, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "INQAIKEGKAAQTERVLRNP", "down_seq": "VALRGVVPDCANGYQRALES", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "156548668", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A636", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q86VI3-1.619.619", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.716.716", "start_pos": 716, "end_pos": 716, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774433919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774433919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774433919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774433919", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774433919", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774433919#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774433919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774433919", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PGCPLNTSHLTREEIQSAVT", "down_seq": "VTAAYDRQQLWKANVGFVIQ", "snv": [ { "evidence": [ { "id": "rs774433919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774433919" }, { "id": "rs774433919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774433919" }, { "id": "rs774433919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774433919#frequency_tab" }, { "id": "rs774433919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774433919" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVT->NVT).", "chr_id": "1", "chr_pos": "156548229", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K716", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q86VI3-1.732.732", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.732.732", "start_pos": 732, "end_pos": 732, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs879547624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879547624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs879547624", "url": "https://www.ncbi.nlm.nih.gov/snp/rs879547624#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs879547624", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879547624", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SAVTKVTAAYDRQQLWKANV", "down_seq": "FVIQLQARLRGFLVRQKFAE", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVG->NVC).", "chr_id": "1", "chr_pos": "156548183", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G732", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs879547624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879547624" }, { "id": "rs879547624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs879547624#frequency_tab" }, { "id": "rs879547624", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879547624" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVG->NVS).", "chr_id": "1", "chr_pos": "156548183", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G732", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86VI3-1.716.716", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.813.813", "start_pos": 813, "end_pos": 813, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AIIKIQAWARMWAARRQYLR", "down_seq": "LHYFQKNVNSIVKIQAFFRA", "snv": [ { "evidence": [ { "id": "Q86VI3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86VI3" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "156544175", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R813", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q86VI3-1.824.824", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.824.824", "start_pos": 824, "end_pos": 824, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769029892", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769029892", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769029892", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769029892", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769029892", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769029892#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769029892", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769029892", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "WAARRQYLRRLHYFQKNVNS", "down_seq": "VKIQAFFRARKAQDDYRILV", "snv": [ { "evidence": [ { "id": "rs769029892", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769029892" }, { "id": "rs769029892", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769029892" }, { "id": "rs769029892", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769029892#frequency_tab" }, { "id": "rs769029892", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769029892" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSI->NST).", "chr_id": "1", "chr_pos": "156544040", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I824", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q86VI3-1.813.813", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.898.898", "start_pos": 898, "end_pos": 898, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1370753468", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370753468", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1370753468", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370753468#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1370753468", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370753468", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "QEEVVRKIRSNQQLEQDLNI", "down_seq": "DIKIGLLVKNRITLQEVVSH", "snv": [ { "evidence": [ { "id": "rs1370753468", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370753468" }, { "id": "rs1370753468", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370753468#frequency_tab" }, { "id": "rs1370753468", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1370753468" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIM->NIT).", "chr_id": "1", "chr_pos": "156540754", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M898", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.997.997", "start_pos": 997, "end_pos": 997, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1362614609", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362614609", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1362614609", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1362614609#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1362614609", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362614609", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MPQNKTTKFMEAVIFSLYNY", "down_seq": "SSRREAYLLLQLFKTALQEE", "snv": [ { "evidence": [ { "id": "rs1362614609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1362614609" }, { "id": "rs1362614609", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1362614609#frequency_tab" }, { "id": "rs1362614609", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1362614609" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYA->NYT).", "chr_id": "1", "chr_pos": "156539441", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A997", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.1135.1135", "start_pos": 1135, "end_pos": 1135, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LDIALRNLLAMTDKFLLAIT", "down_seq": "SVDQIPYGMRYVAKVLKATL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser1135" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q86VI3-1.1136.1136", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1136.1136", "start_pos": 1136, "end_pos": 1136, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DIALRNLLAMTDKFLLAITS", "down_seq": "VDQIPYGMRYVAKVLKATLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser1136" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q86VI3-1.1135.1135", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1360.1360", "start_pos": 1360, "end_pos": 1360, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEVSLTLTNKFEGLEADADD", "down_seq": "NTRSLLLSTKQLLADIIQFH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser1360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q86VI3-1.1358.1358", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86VI3-1.1362.1362", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86VI3-1.1363.1363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "STFFPETTDIYDKKNMPRVV", "down_seq": "CIHALSLFLFRLGLAPQIHD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr140" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q86VI3-1.136.136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1415.1415", "start_pos": 1415, "end_pos": 1415, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "REQEAAHKQLMSRRQACTAQ", "down_seq": "PEPLRRHRSLTAHSLLPLAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Thr1415" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q86VI3-1.1424.1424", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q86VI3-1.1426.1426", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q86VI3-1.1429.1429", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1424.1424", "start_pos": 1424, "end_pos": 1424, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMSRRQACTAQTPEPLRRHR", "down_seq": "LTAHSLLPLAEKQRRVLRNL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser1424" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q86VI3-1.1415.1415", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86VI3-1.1426.1426", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86VI3-1.1429.1429", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86VI3-1.1442.1442", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1426.1426", "start_pos": 1426, "end_pos": 1426, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SRRQACTAQTPEPLRRHRSL", "down_seq": "AHSLLPLAEKQRRVLRNLRR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Thr1426" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q86VI3-1.1415.1415", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86VI3-1.1424.1424", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86VI3-1.1429.1429", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86VI3-1.1442.1442", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86VI3-1.1445.1445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1429.1429", "start_pos": 1429, "end_pos": 1429, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QACTAQTPEPLRRHRSLTAH", "down_seq": "LLPLAEKQRRVLRNLRRLEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1429" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q86VI3-1.1415.1415", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86VI3-1.1424.1424", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q86VI3-1.1426.1426", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q86VI3-1.1442.1442", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86VI3-1.1445.1445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.1537.1537", "start_pos": 1537, "end_pos": 1537, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.", "journal": "Cell", "date": "2007", "authors": "Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DHLAPDSKSSGKGKKQPSLH", "down_seq": "TAAQLLEKGVLVEIEDLPAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" }, { "database": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ], "site_lbl": "Tyr1537" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q86VI3-1.1524.1524", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86VI3-1.1540.1540", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86VI3-1.1556.1556", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86VI3-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IHALSLFLFRLGLAPQIHDL", "down_seq": "GKVKFTAEELSNMASELAKY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "site_lbl": "Tyr162" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q86VI3-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86VI3-1.178.178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86VI3-1.539.539", "start_pos": 539, "end_pos": 539, "uniprot_canonical_ac": "Q86VI3-1", "length": 1631, "uniprot_id": "IQGA3_HUMAN", "protein_name": "Ras GTPase-activating-like protein IQGAP3", "refseq_ac": "", "refseq_name": "", "gene_name": "IQGAP3", "gene_names_uniprotkb": "IQGAP3", "gene_names_refseq": "", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Molecular cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QEETDRVLAVSLINEALDKG", "down_seq": "PEKTLSALLLPAAGLDDVSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86VI3", "url": "https://www.uniprot.org/uniprotkb/Q86VI3" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q86VI3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86VI3" } ], "site_lbl": "Ser539" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "944", "end_pos": "944" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1083", "end_pos": "1083" }, { "start_pos": "1102", "end_pos": "1102" }, { "start_pos": "1238", "end_pos": "1238" }, { "start_pos": "1280", "end_pos": "1280" }, { "start_pos": "1282", "end_pos": "1282" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1442", "end_pos": "1442" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "1524", "end_pos": "1524" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1556", "end_pos": "1556" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1613", "end_pos": "1613" }, { "start_pos": "1618", "end_pos": "1618" }, { "start_pos": "1630", "end_pos": "1630" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "534", "end_pos": "534" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "619", "end_pos": "619" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "898", "end_pos": "898" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "997", "end_pos": "997" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1360", "end_pos": "1360" }, { "start_pos": "1362", "end_pos": "1362" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "1415", "end_pos": "1415" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1426", "end_pos": "1426" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1537", "end_pos": "1537" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "539", "end_pos": "539" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q86VI3-1.534.534", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NYS0-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "Q9NYS0-1", "length": 192, "uniprot_id": "KBRS1_HUMAN", "protein_name": "NF-kappa-B inhibitor-interacting Ras-like protein 1", "refseq_ac": "NP_065078", "refseq_name": "NF-kappa-B inhibitor-interacting Ras-like protein 1 isoform 1", "gene_name": "NKIRAS1", "gene_names_uniprotkb": "NKIRAS1; KBRAS1", "gene_names_refseq": "KBRAS1; NKIRAS1; kappaB-Ras1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NYS0", "url": "https://www.uniprot.org/uniprotkb/Q9NYS0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Inhibition of NF-kappaB activity by IkappaBbeta in association with kappaB-Ras.", "journal": "Molecular and cellular biology", "date": "2004", "authors": "Chen Y, Vallee S, Wu J, Vu D, Sondek J, Ghosh G", "evidence": [ { "database": "UniProtKB", "id": "Q9NYS0", "url": "https://www.uniprot.org/uniprotkb/Q9NYS0" } ], "reference": [ { "type": "PubMed", "id": "15024091", "url": "https://glygen.org/publication/PubMed/15024091" } ] } ], "crossref": [ { "id": "Q9NYS0", "url": "https://www.uniprot.org/uniprotkb/Q9NYS0", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15024091", "url": "https://glygen.org/publication/PubMed/15024091", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TAILEQLLYGNHTIGMEDCE", "down_seq": "MEDVYMASVETDRGVKEQLH", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Loss of function.", "evidence": [ { "database": "UniProtKB", "id": "Q9NYS0", "url": "https://www.uniprot.org/uniprotkb/Q9NYS0" }, { "database": "PubMed", "id": "15024091", "url": "https://glygen.org/publication/PubMed/15024091" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "38", "end_pos": "38" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O60662-1.604.604", "start_pos": 604, "end_pos": 604, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "O60662", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60662" }, { "database": "O-GlcNAc Atlas", "id": "O60662", "url": "https://oglcnac.org/atlas/detail/O60662" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O60662", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60662", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "O60662", "url": "https://oglcnac.org/atlas/detail/O60662", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIRYASGASCLATRLNLFKL", "down_seq": "KL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser604", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "O60662", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O60662" }, { "id": "O60662", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O60662" } ] } ], "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "2", "chr_pos": "169525686", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S604", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O60662-1.602.602", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O60662-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs28763868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs28763868", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs28763868", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs28763868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs28763868", "url": "https://www.ncbi.nlm.nih.gov/snp/rs28763868#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs28763868", "url": "http://gnomad.broadinstitute.org/awesome?query=rs28763868", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KIKVLKDAFAGKLPEPSKNA", "down_seq": "KTGAGEVNGDVGDEDLLPGY", "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" }, { "id": "rs28763868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868" }, { "id": "rs28763868", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs28763868" }, { "id": "rs28763868", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868" }, { "id": "rs28763868", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs28763868#frequency_tab" }, { "id": "rs28763868", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs28763868" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (NAA->NAT).", "chr_id": "2", "chr_pos": "169510589", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A271", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:0110929", "recommended_name": { "id": "DOID:0110929", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110929", "name": "nemaline myopathy 9", "description": "A nemaline myopathy characterized by onset in early infancy of muscle weakness with variable severity that has_material_basis_in homozygous or compound heterozygous mutation in the KLHL41 gene on chromosome 2q31." }, "synonyms": [ { "id": "DOID:0110929", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110929", "name": "NEM9", "description": "" }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "nemaline myopathy 9", "description": "Any nemaline myopathy in which the cause of the disease is a mutation in the KLHL41 gene." }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "KLHL41 nemaline myopathy", "description": "" }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "NEM9", "description": "" }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "nemaline myopathy 9", "description": "" }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "nemaline myopathy caused by mutation in KLHL41", "description": "" }, { "id": "MONDO:0014326", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014326", "name": "nemaline myopathy type 9", "description": "" }, { "id": "MIM:615731", "resource": "MIM", "url": "https://www.omim.org/entry/615731", "name": "Nemaline myopathy 9", "description": "Nemaline myopathy 9" } ], "unlinked_id_list": [], "evidence": [ { "id": "615731", "database": "MIM", "url": "https://www.omim.org/entry/615731" }, { "id": "0110929", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110929" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" }, { "id": "rs28763868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868" }, { "id": "rs28763868", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs28763868" }, { "id": "rs28763868", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28763868" }, { "id": "rs28763868", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs28763868#frequency_tab" }, { "id": "rs28763868", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs28763868" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAA->NAS).", "chr_id": "2", "chr_pos": "169510589", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A271", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VQDIFALASRFQIPSVFTVC", "down_seq": "SYLQKRLAPGNCLAILRLGL", "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "169510145", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V123", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1402907805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402907805", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1402907805", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1402907805#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1402907805", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402907805", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YDPTENECYLTALAEQIPRN", "down_seq": "SSIVTQQNQIYVVGGLYVDE", "snv": [ { "evidence": [ { "id": "rs1402907805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402907805" }, { "id": "rs1402907805", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1402907805#frequency_tab" }, { "id": "rs1402907805", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402907805" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HSS->NSS).", "chr_id": "2", "chr_pos": "169510787", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H337", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1428920171", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1428920171", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1428920171", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1428920171#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1428920171", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1428920171", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YQSTLLQDGLKDLLDEKKFI", "down_seq": "CTLKAGDKSLPCHRLILSAC", "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" }, { "id": "rs1428920171", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1428920171" }, { "id": "rs1428920171", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1428920171#frequency_tab" }, { "id": "rs1428920171", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1428920171" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DCT->NCT).", "chr_id": "2", "chr_pos": "169509878", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D34", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.568.568", "start_pos": 568, "end_pos": 568, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "GGFAMIQLESKEFAPTEVND", "down_seq": "WKYEDDKKEWAGMLKEIRYA", "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDI->NDT).", "chr_id": "2", "chr_pos": "169521001", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I568", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.602.602", "start_pos": 602, "end_pos": 602, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763842140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763842140", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763842140", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763842140", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763842140", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763842140#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763842140", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763842140", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LKEIRYASGASCLATRLNLF", "down_seq": "LSKL", "snv": [ { "evidence": [ { "id": "rs763842140", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763842140" }, { "id": "rs763842140", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763842140" }, { "id": "rs763842140", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763842140#frequency_tab" }, { "id": "rs763842140", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763842140" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "2", "chr_pos": "169525681", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K602", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O60662-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ILSACSPYFREYFLSEIDEA", "down_seq": "KKEVVLDNVDPAILDLIIKY", "snv": [ { "evidence": [ { "id": "O60662", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O60662" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "169509986", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K70", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O60662-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "O60662-1", "length": 606, "uniprot_id": "KLH41_HUMAN", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_006054", "refseq_name": "kelch-like protein 41", "gene_name": "KLHL41", "gene_names_uniprotkb": "KLHL41; KBTBD10; KRP1", "gene_names_refseq": "KBTBD10; KLHL41; Krp1; SARCOSIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MD", "down_seq": "QRELAEELRLYQSTLLQDGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O60662", "url": "https://www.uniprot.org/uniprotkb/O60662" } ], "site_lbl": "Ser3" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "604", "end_pos": "604" } ] }, { "type": "snv", "site_list": [ { "start_pos": "271", "end_pos": "271" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94819-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "O94819-1", "length": 623, "uniprot_id": "KBTBB_HUMAN", "protein_name": "Kelch repeat and BTB domain-containing protein 11", "refseq_ac": "NP_055682", "refseq_name": "kelch repeat and BTB domain-containing protein 11", "gene_name": "KBTBD11", "gene_names_uniprotkb": "KBTBD11; CMLAP; KIAA0711; KLHDC7C", "gene_names_refseq": "KBTBD11; KLHDC7C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94819", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94819", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DADARGDAAVYCFHAAAGEW", "down_seq": "ELTRLPEGAPARGCGLCVLY", "snv": [ { "evidence": [ { "id": "O94819", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O94819" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "2002204", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R338", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "338", "end_pos": "338" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94819-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "O94819-1", "length": 623, "uniprot_id": "KBTBB_HUMAN", "protein_name": "Kelch repeat and BTB domain-containing protein 11", "refseq_ac": "NP_055682", "refseq_name": "kelch repeat and BTB domain-containing protein 11", "gene_name": "KBTBD11", "gene_names_uniprotkb": "KBTBD11; CMLAP; KIAA0711; KLHDC7C", "gene_names_refseq": "KBTBD11; KLHDC7C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" }, { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPEELASPEERACPEEPAAP", "down_seq": "PEPRVWLEDPASPEEPGEPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser107" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "338", "end_pos": "338" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O94819-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O94819-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "O94819-1", "length": 623, "uniprot_id": "KBTBB_HUMAN", "protein_name": "Kelch repeat and BTB domain-containing protein 11", "refseq_ac": "NP_055682", "refseq_name": "kelch repeat and BTB domain-containing protein 11", "gene_name": "KBTBD11", "gene_names_uniprotkb": "KBTBD11; CMLAP; KIAA0711; KLHDC7C", "gene_names_refseq": "KBTBD11; KLHDC7C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSGEESPPQSLASAAEGAAT", "down_seq": "PPSSGGPRVVERQWEAGSAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "site_lbl": "Ser64" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "338", "end_pos": "338" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O94819-1.67.67", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94819-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "O94819-1", "length": 623, "uniprot_id": "KBTBB_HUMAN", "protein_name": "Kelch repeat and BTB domain-containing protein 11", "refseq_ac": "NP_055682", "refseq_name": "kelch repeat and BTB domain-containing protein 11", "gene_name": "KBTBD11", "gene_names_uniprotkb": "KBTBD11; CMLAP; KIAA0711; KLHDC7C", "gene_names_refseq": "KBTBD11; KLHDC7C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EESPPQSLASAAEGAATSPP", "down_seq": "SGGPRVVERQWEAGSAGAAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "site_lbl": "Ser67" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "338", "end_pos": "338" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O94819-1.64.64", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O94819-1.87.87", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O94819-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "O94819-1", "length": 623, "uniprot_id": "KBTBB_HUMAN", "protein_name": "Kelch repeat and BTB domain-containing protein 11", "refseq_ac": "NP_055682", "refseq_name": "kelch repeat and BTB domain-containing protein 11", "gene_name": "KBTBD11", "gene_names_uniprotkb": "KBTBD11; CMLAP; KIAA0711; KLHDC7C", "gene_names_refseq": "KBTBD11; KLHDC7C", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" }, { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSGGPRVVERQWEAGSAGAA", "down_seq": "PEELASPEERACPEEPAAPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O94819", "url": "https://www.uniprot.org/uniprotkb/O94819" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "O94819", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O94819" } ], "site_lbl": "Ser87" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "338", "end_pos": "338" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O94819-1.67.67", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O94819-1.107.107", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50053-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "rs1014338074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1014338074", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1014338074", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1014338074#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DVSQVAWQSKGDTPSSCCII", "down_seq": "NSNGNRTIVLHDTSLPDVSA", "glycosylation": [ { "glytoucan_ac": "G15664MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GDTPSSCCIInNSNGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn102", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GDTPSSCCIInNSNGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn102", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GDTPSSCCIInNSNGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn102", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GDTPSSCCIInNSNGNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn102", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "rs1014338074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1014338074" }, { "id": "rs1014338074", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1014338074#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NNS->SNS); glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094895", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N102", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50053-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1063554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063554", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1063554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063554", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1063554", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063554#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1063554", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063554", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1063554", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063554", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs780202698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780202698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202698", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780202698", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780202698#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780202698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780202698", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QVAWQSKGDTPSSCCIINNS", "down_seq": "GNRTIVLHDTSLPDVSATDF", "snv": [ { "evidence": [ { "id": "rs1063554", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063554" }, { "id": "rs1063554", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063554" }, { "id": "rs1063554", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063554#frequency_tab" }, { "id": "rs1063554", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063554" }, { "id": "rs1063554", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063554" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (NSN->NSS); glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094904", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N105", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs780202698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202698" }, { "id": "rs780202698", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780202698" }, { "id": "rs780202698", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780202698#frequency_tab" }, { "id": "rs780202698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780202698" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094905", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765970509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765970509", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765970509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765970509", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765970509", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765970509", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs774036610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774036610", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774036610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774036610", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774036610", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774036610", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TPSSCCIINNSNGNRTIVLH", "down_seq": "TSLPDVSATDFEKVDLTQFK", "snv": [ { "evidence": [ { "id": "rs765970509", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765970509" }, { "id": "rs765970509", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765970509" }, { "id": "rs765970509", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765970509" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DTS->NTS); glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094930", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D114", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774036610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774036610" }, { "id": "rs774036610", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774036610" }, { "id": "rs774036610", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774036610" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094931", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D114", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670441149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670441149", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670441149", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670441149#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748064599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748064599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748064599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748064599", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748064599", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748064599#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748064599", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748064599", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IHIEGRNASEQVKMLQRIDA", "down_seq": "NTRQPPEQKIRVSVEVEKPR", "snv": [ { "evidence": [ { "id": "rs1670441149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670441149" }, { "id": "rs1670441149", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670441149#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (HNT->NNT); glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097551", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H156", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748064599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748064599" }, { "id": "rs748064599", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748064599" }, { "id": "rs748064599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748064599#frequency_tab" }, { "id": "rs748064599", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748064599" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097552", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H156", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1262799763", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262799763", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1262799763", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262799763#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1262799763", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262799763", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SLSQGRSVQEALRFGCQVAG", "down_seq": "KCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-gain (KKC->NKC); protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099714", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K287", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1262799763", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262799763" }, { "id": "rs1262799763", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262799763#frequency_tab" }, { "id": "rs1262799763", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262799763" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099712", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K287", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular basis of essential fructosuria: molecular cloning and mutational analysis of human ketohexokinase (fructokinase).", "journal": "Human molecular genetics", "date": "1994", "authors": "Bonthron DT, Brady N, Donaldson IA, Steinmann B", "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" }, { "database": "Reactome", "id": "R-HSA-70350", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-70350" }, { "database": "dbSNP", "id": "rs104893643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643" }, { "database": "dbSNP", "id": "rs104893644", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644" } ], "reference": [ { "type": "PubMed", "id": "7833921", "url": "https://glygen.org/publication/PubMed/7833921" } ] } ], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs104893644", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs104893644", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs104893644", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104893644#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs104893644", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104893644", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "7833921", "url": "https://glygen.org/publication/PubMed/7833921", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs104893644", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104893644", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs773093592", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773093592", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773093592", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773093592#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773093592", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773093592", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs773093592", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773093592", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YPKEDSEIRCLSQRWQRGGN", "down_seq": "SNSCTVLSLLGAPCAFMGSM", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs104893644", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644" }, { "id": "rs104893644", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644" }, { "id": "rs104893644", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104893644#frequency_tab" }, { "id": "rs104893644", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104893644" }, { "id": "7833921", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/7833921" }, { "id": "rs104893644", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104893644" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "5", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092366", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A43", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs773093592", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592" }, { "id": "rs773093592", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592" }, { "id": "rs773093592", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773093592#frequency_tab" }, { "id": "rs773093592", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773093592" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092367", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A43", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773093592", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592" }, { "id": "rs773093592", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773093592" }, { "id": "rs773093592", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773093592#frequency_tab" }, { "id": "rs773093592", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773093592" }, { "id": "rs773093592", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773093592" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092367", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A43", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50053-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2304681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2304681", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs2304681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs2304681", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2304681#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2304681", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2304681", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2304681", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EIRCLSQRWQRGGNASNSCT", "down_seq": "LSLLGAPCAFMGSMAPGHVA", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs2304681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681" }, { "id": "rs2304681", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2304681#frequency_tab" }, { "id": "rs2304681", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2304681" }, { "id": "rs2304681", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092384", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V49", "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ], "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ] }, { "evidence": [ { "id": "rs2304681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681" }, { "id": "rs2304681", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2304681#frequency_tab" }, { "id": "rs2304681", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2304681" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092384", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V49", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2304681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2304681" }, { "id": "rs2304681", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2304681" }, { "id": "rs2304681", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2304681#frequency_tab" }, { "id": "rs2304681", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2304681" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092384", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200568467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200568467", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200568467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200568467", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200568467", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200568467#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200568467", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200568467", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CAFMGSMAPGHVADFLVADF", "down_seq": "RRGVDVSQVAWQSKGDTPSS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094496", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R77", "keywords": [ "biomuta", "somatic", "cancer" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094497", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R77", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs200568467", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200568467" }, { "id": "rs200568467", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200568467" }, { "id": "rs200568467", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200568467#frequency_tab" }, { "id": "rs200568467", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200568467" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094819", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R77", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1163780326", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1163780326", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1163780326", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1163780326", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQVAWQSKGDTPSSCCIINN", "down_seq": "NGNRTIVLHDTSLPDVSATD", "snv": [ { "evidence": [ { "id": "rs1163780326", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1163780326" }, { "id": "rs1163780326", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1163780326" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094901", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747107883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747107883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747107883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747107883", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747107883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747107883", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VAWQSKGDTPSSCCIINNSN", "down_seq": "NRTIVLHDTSLPDVSATDFE", "snv": [ { "evidence": [ { "id": "rs747107883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747107883" }, { "id": "rs747107883", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747107883" }, { "id": "rs747107883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747107883" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094907", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs202073910", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202073910", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202073910", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202073910#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202073910", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202073910", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768749071", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768749071", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768749071", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768749071#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768749071", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768749071", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WQSKGDTPSSCCIINNSNGN", "down_seq": "TIVLHDTSLPDVSATDFEKV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs202073910", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202073910" }, { "id": "rs202073910", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202073910#frequency_tab" }, { "id": "rs202073910", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202073910" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094912", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R108", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs768749071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071" }, { "id": "rs768749071", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071" }, { "id": "rs768749071", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768749071#frequency_tab" }, { "id": "rs768749071", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768749071" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094590", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R108", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs768749071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071" }, { "id": "rs768749071", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768749071" }, { "id": "rs768749071", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768749071#frequency_tab" }, { "id": "rs768749071", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768749071" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094913", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R108", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs202073910", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202073910" }, { "id": "rs202073910", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202073910#frequency_tab" }, { "id": "rs202073910", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202073910" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094912", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs370901888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370901888", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370901888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370901888", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370901888", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370901888#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370901888", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370901888", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs370901888", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs370901888", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QSKGDTPSSCCIINNSNGNR", "down_seq": "IVLHDTSLPDVSATDFEKVD", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs370901888", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370901888" }, { "id": "rs370901888", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370901888" }, { "id": "rs370901888", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370901888#frequency_tab" }, { "id": "rs370901888", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370901888" }, { "id": "rs370901888", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs370901888" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094916", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T109", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MEEKQILCV", "down_seq": "LVVLDVISLVDKYPKEDSEI", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087287", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "G10", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087287", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G10", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368515189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368515189", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368515189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368515189", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368515189", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368515189#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368515189", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368515189", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SKGDTPSSCCIINNSNGNRT", "down_seq": "VLHDTSLPDVSATDFEKVDL", "snv": [ { "evidence": [ { "id": "rs368515189", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368515189" }, { "id": "rs368515189", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368515189" }, { "id": "rs368515189", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368515189#frequency_tab" }, { "id": "rs368515189", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368515189" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094918", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs548115211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs548115211", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548115211", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs548115211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs548115211", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548115211#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs548115211", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548115211", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs553107212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553107212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs553107212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553107212", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs553107212", "url": "https://www.ncbi.nlm.nih.gov/snp/rs553107212#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs553107212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs553107212", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DTPSSCCIINNSNGNRTIVL", "down_seq": "DTSLPDVSATDFEKVDLTQF", "snv": [ { "evidence": [ { "id": "rs548115211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211" }, { "id": "rs548115211", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548115211" }, { "id": "rs548115211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211" }, { "id": "rs548115211", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548115211#frequency_tab" }, { "id": "rs548115211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548115211" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094928", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H113", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs548115211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211" }, { "id": "rs548115211", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548115211" }, { "id": "rs548115211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548115211" }, { "id": "rs548115211", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548115211#frequency_tab" }, { "id": "rs548115211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548115211" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094928", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H113", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs553107212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553107212" }, { "id": "rs553107212", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs553107212" }, { "id": "rs553107212", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs553107212#frequency_tab" }, { "id": "rs553107212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs553107212" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094927", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "H113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670247490", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670247490", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670247490", "url": "https://www.ensembl.org/id/rs1670247490", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1140588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1140588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1140588", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1140588#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1140588", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1140588", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSSCCIINNSNGNRTIVLHD", "down_seq": "SLPDVSATDFEKVDLTQFKW", "snv": [ { "evidence": [ { "id": "rs1670247490", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670247490" }, { "id": "rs1670247490", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670247490" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094933", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1140588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588" }, { "id": "rs1140588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588" }, { "id": "rs1140588", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1140588#frequency_tab" }, { "id": "rs1140588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1140588" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094934", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1140588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588" }, { "id": "rs1140588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1140588" }, { "id": "rs1140588", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1140588#frequency_tab" }, { "id": "rs1140588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1140588" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094934", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774999673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774999673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774999673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774999673", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774999673", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774999673", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1386498526", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386498526", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1386498526", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386498526", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSCCIINNSNGNRTIVLHDT", "down_seq": "LPDVSATDFEKVDLTQFKWI", "snv": [ { "evidence": [ { "id": "rs774999673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774999673" }, { "id": "rs774999673", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774999673" }, { "id": "rs774999673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774999673" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096730", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1386498526", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386498526" }, { "id": "rs1386498526", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386498526" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096731", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1173075290", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173075290", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1173075290", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1173075290#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1173075290", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173075290", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1173075290", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1173075290", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CCIINNSNGNRTIVLHDTSL", "down_seq": "DVSATDFEKVDLTQFKWIHI", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1173075290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173075290" }, { "id": "rs1173075290", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1173075290#frequency_tab" }, { "id": "rs1173075290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173075290" }, { "id": "rs1173075290", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1173075290" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096736", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P118", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760708527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760708527", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760708527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760708527", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760708527", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760708527#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760708527", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760708527", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1558448733", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558448733", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1558448733", "url": "https://www.ensembl.org/id/rs1558448733", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INNSNGNRTIVLHDTSLPDV", "down_seq": "ATDFEKVDLTQFKWIHIEGR", "snv": [ { "evidence": [ { "id": "rs760708527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760708527" }, { "id": "rs760708527", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760708527" }, { "id": "rs760708527", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760708527#frequency_tab" }, { "id": "rs760708527", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760708527" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096746", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S121", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1558448733", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558448733" }, { "id": "rs1558448733", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1558448733" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096745", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1319171317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319171317", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1319171317", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1319171317", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NNSNGNRTIVLHDTSLPDVS", "down_seq": "TDFEKVDLTQFKWIHIEGRN", "snv": [ { "evidence": [ { "id": "rs1319171317", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319171317" }, { "id": "rs1319171317", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1319171317" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096748", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A122", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SNGNRTIVLHDTSLPDVSAT", "down_seq": "FEKVDLTQFKWIHIEGRNAS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096754", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D124", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764174512", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764174512", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764174512", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764174512", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764174512", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764174512", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GNRTIVLHDTSLPDVSATDF", "down_seq": "KVDLTQFKWIHIEGRNASEQ", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs764174512", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764174512" }, { "id": "rs764174512", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764174512" }, { "id": "rs764174512", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764174512" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096760", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E126", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761767044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761767044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761767044", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761767044#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761767044", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761767044", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1670379174", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670379174", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670379174", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670379174", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RTIVLHDTSLPDVSATDFEK", "down_seq": "DLTQFKWIHIEGRNASEQVK", "snv": [ { "evidence": [ { "id": "rs761767044", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044" }, { "id": "rs761767044", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044" }, { "id": "rs761767044", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761767044#frequency_tab" }, { "id": "rs761767044", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761767044" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096767", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761767044", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044" }, { "id": "rs761767044", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761767044" }, { "id": "rs761767044", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761767044#frequency_tab" }, { "id": "rs761767044", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761767044" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096767", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1670379174", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670379174" }, { "id": "rs1670379174", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670379174" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096766", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V128", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670379559", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670379559", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670379559", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670379559", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TIVLHDTSLPDVSATDFEKV", "down_seq": "LTQFKWIHIEGRNASEQVKM", "snv": [ { "evidence": [ { "id": "rs1670379559", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670379559" }, { "id": "rs1670379559", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670379559" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096769", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D129", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755245908", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755245908", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755245908", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755245908", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755245908", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755245908#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755245908", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755245908", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MEEKQILCVGL", "down_seq": "VLDVISLVDKYPKEDSEIRC", "snv": [ { "evidence": [ { "id": "rs755245908", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755245908" }, { "id": "rs755245908", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755245908" }, { "id": "rs755245908", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755245908#frequency_tab" }, { "id": "rs755245908", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755245908" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087293", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V12", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1347233409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347233409", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1347233409", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347233409", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "IVLHDTSLPDVSATDFEKVD", "down_seq": "TQFKWIHIEGRNASEQVKML", "snv": [ { "evidence": [ { "id": "rs1347233409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347233409" }, { "id": "rs1347233409", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347233409" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096773", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096773", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L130", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs755158028", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755158028", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755158028", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755158028", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755158028", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755158028#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755158028", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755158028", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs755158028", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs755158028", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LHDTSLPDVSATDFEKVDLT", "down_seq": "FKWIHIEGRNASEQVKMLQR", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs755158028", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755158028" }, { "id": "rs755158028", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755158028" }, { "id": "rs755158028", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755158028#frequency_tab" }, { "id": "rs755158028", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755158028" }, { "id": "rs755158028", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs755158028" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096780", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q132", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781159945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781159945", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781159945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781159945", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781159945", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781159945", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "HDTSLPDVSATDFEKVDLTQ", "down_seq": "KWIHIEGRNASEQVKMLQRI", "snv": [ { "evidence": [ { "id": "rs781159945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781159945" }, { "id": "rs781159945", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781159945" }, { "id": "rs781159945", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781159945" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096781", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F133", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LPDVSATDFEKVDLTQFKWI", "down_seq": "IEGRNASEQVKMLQRIDAHN", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "H", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27096795", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H137", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1326418810", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1326418810", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1326418810", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1326418810", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PDVSATDFEKVDLTQFKWIH", "down_seq": "EGRNASEQVKMLQRIDAHNT", "snv": [ { "evidence": [ { "id": "rs1326418810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1326418810" }, { "id": "rs1326418810", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1326418810" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096797", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I138", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.139.139", "start_pos": 139, "end_pos": 139, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1206403617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206403617", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1206403617", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206403617", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DVSATDFEKVDLTQFKWIHI", "down_seq": "GRNASEQVKMLQRIDAHNTR", "snv": [ { "evidence": [ { "id": "rs1206403617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206403617" }, { "id": "rs1206403617", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206403617" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27096799", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E139", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs767831413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767831413", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767831413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767831413", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767831413", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767831413#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767831413", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767831413", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs767831413", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs767831413", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs562642551", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562642551", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs562642551", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs562642551", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs562642551", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562642551", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs562642551", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562642551#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs562642551", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562642551", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SATDFEKVDLTQFKWIHIEG", "down_seq": "NASEQVKMLQRIDAHNTRQP", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs767831413", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767831413" }, { "id": "rs767831413", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767831413" }, { "id": "rs767831413", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767831413#frequency_tab" }, { "id": "rs767831413", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767831413" }, { "id": "rs767831413", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs767831413" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097507", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R141", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs562642551", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562642551" }, { "id": "rs562642551", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs562642551" }, { "id": "rs562642551", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562642551" }, { "id": "rs562642551", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562642551#frequency_tab" }, { "id": "rs562642551", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562642551" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097506", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "R141", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201014038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201014038", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201014038", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201014038#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201014038", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201014038", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201014038", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201014038", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TDFEKVDLTQFKWIHIEGRN", "down_seq": "SEQVKMLQRIDAHNTRQPPE", "snv": [ { "evidence": [ { "id": "rs201014038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201014038" }, { "id": "rs201014038", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201014038#frequency_tab" }, { "id": "rs201014038", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201014038" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097512", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A143", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs201014038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201014038" }, { "id": "rs201014038", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201014038#frequency_tab" }, { "id": "rs201014038", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201014038" }, { "id": "rs201014038", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201014038" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097512", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A143", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756258011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756258011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756258011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756258011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756258011", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756258011", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1349702820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349702820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1349702820", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349702820#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1349702820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349702820", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DFEKVDLTQFKWIHIEGRNA", "down_seq": "EQVKMLQRIDAHNTRQPPEQ", "snv": [ { "evidence": [ { "id": "rs756258011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756258011#frequency_tab" }, { "id": "rs756258011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756258011" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097516", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1349702820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349702820" }, { "id": "rs1349702820", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349702820#frequency_tab" }, { "id": "rs1349702820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349702820" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097515", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756258011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756258011#frequency_tab" }, { "id": "rs756258011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756258011" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097516", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097515", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S144", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs756258011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756258011" }, { "id": "rs756258011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756258011#frequency_tab" }, { "id": "rs756258011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756258011" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097516", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757718324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718324", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757718324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718324", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757718324", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757718324", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1329503329", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329503329", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1329503329", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329503329", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs779178929", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779178929", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779178929", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779178929", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779178929", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779178929#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779178929", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779178929", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "FEKVDLTQFKWIHIEGRNAS", "down_seq": "QVKMLQRIDAHNTRQPPEQK", "snv": [ { "evidence": [ { "id": "rs757718324", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718324" }, { "id": "rs757718324", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718324" }, { "id": "rs757718324", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757718324" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097518", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1329503329", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329503329" }, { "id": "rs1329503329", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329503329" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097520", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097518", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E145", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs779178929", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779178929" }, { "id": "rs779178929", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779178929" }, { "id": "rs779178929", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779178929#frequency_tab" }, { "id": "rs779178929", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779178929" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097519", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "EKVDLTQFKWIHIEGRNASE", "down_seq": "VKMLQRIDAHNTRQPPEQKI", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097523", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q146", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097522", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Q146", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs533090879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs533090879", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs533090879", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs533090879", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs533090879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs533090879", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs533090879", "url": "http://gnomad.broadinstitute.org/awesome?query=rs533090879", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VDLTQFKWIHIEGRNASEQV", "down_seq": "MLQRIDAHNTRQPPEQKIRV", "snv": [ { "evidence": [ { "id": "rs533090879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs533090879" }, { "id": "rs533090879", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs533090879" }, { "id": "rs533090879", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs533090879" }, { "id": "rs533090879", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs533090879" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097527", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K148", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670437912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670437912", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670437912", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670437912#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670437912", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670437912", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "DLTQFKWIHIEGRNASEQVK", "down_seq": "LQRIDAHNTRQPPEQKIRVS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1670437912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670437912" }, { "id": "rs1670437912", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670437912#frequency_tab" }, { "id": "rs1670437912", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670437912" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097532", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M149", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs773283064", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773283064", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773283064", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773283064", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MEEKQILCVGLVV", "down_seq": "DVISLVDKYPKEDSEIRCLS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087299", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L14", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs773283064", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773283064" }, { "id": "rs773283064", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773283064" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087299", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670438143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670438143", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670438143", "url": "https://www.ensembl.org/id/rs1670438143", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LTQFKWIHIEGRNASEQVKM", "down_seq": "QRIDAHNTRQPPEQKIRVSV", "snv": [ { "evidence": [ { "id": "rs1670438143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670438143" }, { "id": "rs1670438143", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670438143" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097533", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1242006155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242006155", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1242006155", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1242006155#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1242006155", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242006155", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "TQFKWIHIEGRNASEQVKML", "down_seq": "RIDAHNTRQPPEQKIRVSVE", "snv": [ { "evidence": [ { "id": "rs1242006155", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1242006155" }, { "id": "rs1242006155", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1242006155#frequency_tab" }, { "id": "rs1242006155", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1242006155" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097537", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs377146926", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377146926", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377146926", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377146926", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377146926", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377146926#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377146926", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377146926", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs377146926", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs377146926", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1359714770", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359714770", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1359714770", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1359714770#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1359714770", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359714770", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QFKWIHIEGRNASEQVKMLQ", "down_seq": "IDAHNTRQPPEQKIRVSVEV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097540", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R152", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs377146926", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377146926" }, { "id": "rs377146926", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377146926" }, { "id": "rs377146926", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377146926#frequency_tab" }, { "id": "rs377146926", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377146926" }, { "id": "rs377146926", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs377146926" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097540", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R152", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1359714770", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359714770" }, { "id": "rs1359714770", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1359714770#frequency_tab" }, { "id": "rs1359714770", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359714770" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097539", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R152", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1272917989", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272917989", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1272917989", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272917989", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1272917989", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1272917989", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FKWIHIEGRNASEQVKMLQR", "down_seq": "DAHNTRQPPEQKIRVSVEVE", "snv": [ { "evidence": [ { "id": "rs1272917989", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272917989" }, { "id": "rs1272917989", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272917989" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097543", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I153", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1272917989", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272917989" }, { "id": "rs1272917989", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272917989" }, { "id": "rs1272917989", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1272917989" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097543", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I153", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1342429529", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342429529", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1342429529", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1342429529", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs746646647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746646647", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746646647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746646647", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746646647", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746646647#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746646647", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746646647", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KWIHIEGRNASEQVKMLQRI", "down_seq": "AHNTRQPPEQKIRVSVEVEK", "snv": [ { "evidence": [ { "id": "rs1342429529", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1342429529" }, { "id": "rs1342429529", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1342429529" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097546", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D154", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746646647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746646647" }, { "id": "rs746646647", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746646647" }, { "id": "rs746646647", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746646647#frequency_tab" }, { "id": "rs746646647", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746646647" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097545", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D154", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs933339831", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933339831", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs933339831", "url": "http://gnomad.broadinstitute.org/awesome?query=rs933339831", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs776211460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776211460", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776211460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776211460", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776211460", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776211460#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776211460", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776211460", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs776211460", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs776211460", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "WIHIEGRNASEQVKMLQRID", "down_seq": "HNTRQPPEQKIRVSVEVEKP", "snv": [ { "evidence": [ { "id": "rs933339831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933339831" }, { "id": "rs933339831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs933339831" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097549", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs776211460", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776211460" }, { "id": "rs776211460", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776211460" }, { "id": "rs776211460", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776211460#frequency_tab" }, { "id": "rs776211460", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776211460" }, { "id": "rs776211460", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs776211460" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097548", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A155", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs933339831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs933339831" }, { "id": "rs933339831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs933339831" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097549", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs150233686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150233686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150233686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150233686", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150233686", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150233686#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150233686", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150233686", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HIEGRNASEQVKMLQRIDAH", "down_seq": "TRQPPEQKIRVSVEVEKPRE", "snv": [ { "evidence": [ { "id": "rs150233686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150233686" }, { "id": "rs150233686", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150233686" }, { "id": "rs150233686", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150233686#frequency_tab" }, { "id": "rs150233686", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150233686" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097555", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N157", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773003580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773003580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773003580", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773003580#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773003580", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773003580", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1572874480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572874480", "url": "https://www.ensembl.org/id/rs1572874480", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IEGRNASEQVKMLQRIDAHN", "down_seq": "RQPPEQKIRVSVEVEKPREE", "snv": [ { "evidence": [ { "id": "rs773003580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580" }, { "id": "rs773003580", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580" }, { "id": "rs773003580", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773003580#frequency_tab" }, { "id": "rs773003580", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773003580" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097558", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T158", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773003580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580" }, { "id": "rs773003580", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773003580" }, { "id": "rs773003580", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773003580#frequency_tab" }, { "id": "rs773003580", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773003580" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097558", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T158", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1572874480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874480" }, { "id": "rs1572874480", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572874480" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097557", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T158", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs762849530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762849530", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762849530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762849530", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762849530", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762849530#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762849530", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762849530", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EGRNASEQVKMLQRIDAHNT", "down_seq": "QPPEQKIRVSVEVEKPREEL", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs762849530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762849530" }, { "id": "rs762849530", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762849530" }, { "id": "rs762849530", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762849530#frequency_tab" }, { "id": "rs762849530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762849530" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097561", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R159", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GRNASEQVKMLQRIDAHNTR", "down_seq": "PPEQKIRVSVEVEKPREELF", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097564", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q160", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NASEQVKMLQRIDAHNTRQP", "down_seq": "EQKIRVSVEVEKPREELFQL", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097570", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P162", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1463357817", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463357817", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1463357817", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1463357817#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1463357817", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463357817", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ASEQVKMLQRIDAHNTRQPP", "down_seq": "QKIRVSVEVEKPREELFQLF", "snv": [ { "evidence": [ { "id": "rs1463357817", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463357817" }, { "id": "rs1463357817", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1463357817#frequency_tab" }, { "id": "rs1463357817", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463357817" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097573", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E163", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766162588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766162588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766162588", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766162588", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775751684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775751684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775751684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775751684", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775751684", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775751684#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775751684", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775751684", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SEQVKMLQRIDAHNTRQPPE", "down_seq": "KIRVSVEVEKPREELFQLFG", "snv": [ { "evidence": [ { "id": "rs766162588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588" }, { "id": "rs766162588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588" }, { "id": "rs766162588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766162588" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097575", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q164", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775751684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775751684" }, { "id": "rs775751684", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775751684" }, { "id": "rs775751684", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775751684#frequency_tab" }, { "id": "rs775751684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775751684" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097577", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q164", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766162588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588" }, { "id": "rs766162588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766162588" }, { "id": "rs766162588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766162588" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097575", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q164", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670443308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670443308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670443308", "url": "https://www.ensembl.org/id/rs1670443308", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1393724290", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393724290", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1393724290", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393724290", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EQVKMLQRIDAHNTRQPPEQ", "down_seq": "IRVSVEVEKPREELFQLFGY", "snv": [ { "evidence": [ { "id": "rs1670443308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670443308" }, { "id": "rs1670443308", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670443308" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097578", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K165", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097580", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K165", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1393724290", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393724290" }, { "id": "rs1393724290", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393724290" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097579", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K165", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201707861", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201707861", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201707861", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201707861", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201707861#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201707861", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201707861", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201707861", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs886055887", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055887", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886055887", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886055887", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VKMLQRIDAHNTRQPPEQKI", "down_seq": "VSVEVEKPREELFQLFGYGD", "snv": [ { "evidence": [ { "id": "rs201707861", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861" }, { "id": "rs201707861", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861" }, { "id": "rs201707861", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861" }, { "id": "rs201707861", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201707861#frequency_tab" }, { "id": "rs201707861", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201707861" }, { "id": "rs201707861", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097585", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R167", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs201707861", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861" }, { "id": "rs201707861", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861" }, { "id": "rs201707861", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201707861" }, { "id": "rs201707861", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201707861#frequency_tab" }, { "id": "rs201707861", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201707861" }, { "id": "rs201707861", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201707861" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097585", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R167", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs886055887", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055887" }, { "id": "rs886055887", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886055887" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "5", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097584", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R167", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765811812", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765811812", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765811812", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765811812", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765811812", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765811812", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs757728460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757728460", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757728460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757728460", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757728460", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757728460", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "KMLQRIDAHNTRQPPEQKIR", "down_seq": "SVEVEKPREELFQLFGYGDV", "snv": [ { "evidence": [ { "id": "rs765811812", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765811812" }, { "id": "rs765811812", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765811812" }, { "id": "rs765811812", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765811812" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097588", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V168", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757728460", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757728460" }, { "id": "rs757728460", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757728460" }, { "id": "rs757728460", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757728460" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097587", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V168", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371146138#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371146138", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LQRIDAHNTRQPPEQKIRVS", "down_seq": "EVEKPREELFQLFGYGDVVF", "snv": [ { "evidence": [ { "id": "rs371146138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" }, { "id": "rs371146138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371146138#frequency_tab" }, { "id": "rs371146138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371146138" }, { "id": "rs371146138", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097593", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V170", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs371146138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" }, { "id": "rs371146138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371146138#frequency_tab" }, { "id": "rs371146138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371146138" }, { "id": "rs371146138", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097593", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V170", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1572874681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874681", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572874681", "url": "https://www.ensembl.org/id/rs1572874681", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RIDAHNTRQPPEQKIRVSVE", "down_seq": "EKPREELFQLFGYGDVVFVS", "snv": [ { "evidence": [ { "id": "rs1572874681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874681" }, { "id": "rs1572874681", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572874681" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097600", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780869692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780869692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780869692", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780869692#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780869692", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780869692", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1464530815", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464530815", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1464530815", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464530815", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AHNTRQPPEQKIRVSVEVEK", "down_seq": "REELFQLFGYGDVVFVSKDV", "snv": [ { "evidence": [ { "id": "rs780869692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692" }, { "id": "rs780869692", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692" }, { "id": "rs780869692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780869692#frequency_tab" }, { "id": "rs780869692", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780869692" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097608", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P175", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1464530815", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464530815" }, { "id": "rs1464530815", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464530815" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097609", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P175", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs780869692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692" }, { "id": "rs780869692", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780869692" }, { "id": "rs780869692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780869692#frequency_tab" }, { "id": "rs780869692", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780869692" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097608", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P175", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199554107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199554107", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199554107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199554107", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199554107", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199554107#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199554107", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199554107", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199554107", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199554107", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143669793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143669793", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143669793", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143669793#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143669793", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs143669793", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143669793", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HNTRQPPEQKIRVSVEVEKP", "down_seq": "EELFQLFGYGDVVFVSKDVA", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs199554107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199554107" }, { "id": "rs199554107", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199554107" }, { "id": "rs199554107", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199554107#frequency_tab" }, { "id": "rs199554107", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199554107" }, { "id": "rs199554107", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199554107" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097611", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R176", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs143669793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143669793" }, { "id": "rs143669793", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143669793" }, { "id": "rs143669793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143669793" }, { "id": "rs143669793", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143669793#frequency_tab" }, { "id": "rs143669793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143669793" }, { "id": "rs143669793", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143669793" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097612", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R176", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670450121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670450121", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670450121", "url": "https://www.ensembl.org/id/rs1670450121", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TRQPPEQKIRVSVEVEKPRE", "down_seq": "LFQLFGYGDVVFVSKDVAKH", "snv": [ { "evidence": [ { "id": "rs1670450121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670450121" }, { "id": "rs1670450121", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670450121" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097619", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E178", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1572874792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572874792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1572874792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1572874792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1572874792", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1430018124", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1430018124", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1430018124", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1430018124#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1430018124", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1430018124", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "QPPEQKIRVSVEVEKPREEL", "down_seq": "QLFGYGDVVFVSKDVAKHLG", "snv": [ { "evidence": [ { "id": "rs1572874792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572874792" }, { "id": "rs1572874792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1572874792#frequency_tab" }, { "id": "rs1572874792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1572874792" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097625", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F180", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1430018124", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1430018124" }, { "id": "rs1430018124", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1430018124#frequency_tab" }, { "id": "rs1430018124", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1430018124" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097624", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F180", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PPEQKIRVSVEVEKPREELF", "down_seq": "LFGYGDVVFVSKDVAKHLGF", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097626", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q181", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097628", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q181", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773270820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773270820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773270820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773270820", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773270820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773270820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "EQKIRVSVEVEKPREELFQL", "down_seq": "GYGDVVFVSKDVAKHLGFQS", "snv": [ { "evidence": [ { "id": "rs773270820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773270820" }, { "id": "rs773270820", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773270820" }, { "id": "rs773270820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773270820" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097633", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F183", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142728562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142728562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142728562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142728562", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142728562", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142728562#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142728562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142728562", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QKIRVSVEVEKPREELFQLF", "down_seq": "YGDVVFVSKDVAKHLGFQSA", "snv": [ { "evidence": [ { "id": "rs142728562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142728562" }, { "id": "rs142728562", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142728562" }, { "id": "rs142728562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142728562#frequency_tab" }, { "id": "rs142728562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142728562" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097636", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138841298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138841298", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138841298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138841298", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138841298", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138841298#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138841298", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138841298", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KIRVSVEVEKPREELFQLFG", "down_seq": "GDVVFVSKDVAKHLGFQSAE", "snv": [ { "evidence": [ { "id": "rs138841298", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138841298" }, { "id": "rs138841298", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138841298" }, { "id": "rs138841298", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138841298#frequency_tab" }, { "id": "rs138841298", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138841298" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097639", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y185", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs886055888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055888", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886055888", "url": "https://www.ensembl.org/id/rs886055888", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs372208973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372208973", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372208973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372208973", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372208973", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372208973#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372208973", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372208973", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "IRVSVEVEKPREELFQLFGY", "down_seq": "DVVFVSKDVAKHLGFQSAEE", "snv": [ { "evidence": [ { "id": "rs886055888", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055888" }, { "id": "rs886055888", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs886055888" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097642", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G186", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs372208973", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372208973" }, { "id": "rs372208973", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372208973" }, { "id": "rs372208973", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372208973#frequency_tab" }, { "id": "rs372208973", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372208973" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097641", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G186", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs41288797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41288797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs41288797", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs41288797", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs41288797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41288797", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs41288797", "url": "https://www.ncbi.nlm.nih.gov/snp/rs41288797#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs41288797", "url": "http://gnomad.broadinstitute.org/awesome?query=rs41288797", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VSVEVEKPREELFQLFGYGD", "down_seq": "VFVSKDVAKHLGFQSAEEAL", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27097647", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V188", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs41288797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41288797" }, { "id": "rs41288797", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs41288797" }, { "id": "rs41288797", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41288797" }, { "id": "rs41288797", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs41288797#frequency_tab" }, { "id": "rs41288797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs41288797" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27097647", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V188", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs879019463", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879019463", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs879019463", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879019463", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SVEVEKPREELFQLFGYGDV", "down_seq": "FVSKDVAKHLGFQSAEEALR", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099197", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V189", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs879019463", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs879019463" }, { "id": "rs879019463", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs879019463" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099196", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V189", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756218495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756218495", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756218495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756218495", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756218495", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756218495", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs756218495", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756218495", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEEKQILCVGLVVLDVI", "down_seq": "LVDKYPKEDSEIRCLSQRWQ", "snv": [ { "evidence": [ { "id": "rs756218495", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756218495" }, { "id": "rs756218495", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756218495" }, { "id": "rs756218495", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756218495" }, { "id": "rs756218495", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756218495" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087312", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S18", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670615826", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670615826", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670615826", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670615826", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VEVEKPREELFQLFGYGDVV", "down_seq": "VSKDVAKHLGFQSAEEALRG", "snv": [ { "evidence": [ { "id": "rs1670615826", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670615826" }, { "id": "rs1670615826", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670615826" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099201", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F190", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1409506909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409506909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1409506909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1409506909", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1175471954", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175471954", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1175471954", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175471954", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EVEKPREELFQLFGYGDVVF", "down_seq": "SKDVAKHLGFQSAEEALRGL", "snv": [ { "evidence": [ { "id": "rs1409506909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409506909" }, { "id": "rs1409506909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1409506909" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099203", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V191", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1175471954", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1175471954" }, { "id": "rs1175471954", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1175471954" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099202", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V191", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760045793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760045793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760045793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760045793", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VEKPREELFQLFGYGDVVFV", "down_seq": "KDVAKHLGFQSAEEALRGLY", "snv": [ { "evidence": [ { "id": "rs760045793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793" }, { "id": "rs760045793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793" }, { "id": "rs760045793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760045793" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099205", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S192", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760045793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793" }, { "id": "rs760045793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760045793" }, { "id": "rs760045793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760045793" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099205", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S192", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670616998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670616998", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670616998", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670616998#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EKPREELFQLFGYGDVVFVS", "down_seq": "DVAKHLGFQSAEEALRGLYG", "snv": [ { "evidence": [ { "id": "rs1670616998", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670616998" }, { "id": "rs1670616998", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670616998#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099208", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767761539", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767761539", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767761539", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767761539", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KPREELFQLFGYGDVVFVSK", "down_seq": "VAKHLGFQSAEEALRGLYGR", "snv": [ { "evidence": [ { "id": "rs767761539", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539" }, { "id": "rs767761539", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539" }, { "id": "rs767761539", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767761539" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099211", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D194", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767761539", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539" }, { "id": "rs767761539", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767761539" }, { "id": "rs767761539", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767761539" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099211", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D194", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.175.175", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1426869673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426869673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1426869673", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426869673", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EELFQLFGYGDVVFVSKDVA", "down_seq": "HLGFQSAEEALRGLYGRVRK", "snv": [ { "evidence": [ { "id": "rs1426869673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426869673" }, { "id": "rs1426869673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426869673" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099221", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670618451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670618451", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670618451", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670618451#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LFQLFGYGDVVFVSKDVAKH", "down_seq": "GFQSAEEALRGLYGRVRKGA", "snv": [ { "evidence": [ { "id": "rs1670618451", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670618451" }, { "id": "rs1670618451", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670618451#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099227", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L199", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1304124716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1304124716", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1304124716", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1304124716", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1304124716", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1304124716", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "QLFGYGDVVFVSKDVAKHLG", "down_seq": "QSAEEALRGLYGRVRKGAVL", "snv": [ { "evidence": [ { "id": "rs1304124716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1304124716" }, { "id": "rs1304124716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1304124716" }, { "id": "rs1304124716", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1304124716" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099232", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F201", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755659806", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755659806", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755659806", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755659806", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755659806", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755659806", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1440617212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1440617212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1440617212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1440617212", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LFGYGDVVFVSKDVAKHLGF", "down_seq": "SAEEALRGLYGRVRKGAVLV", "snv": [ { "evidence": [ { "id": "rs755659806", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755659806" }, { "id": "rs755659806", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755659806" }, { "id": "rs755659806", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755659806" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099235", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q202", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1440617212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1440617212" }, { "id": "rs1440617212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1440617212" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099236", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q202", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1558452514", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558452514", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1558452514", "url": "https://www.ensembl.org/id/rs1558452514", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGYGDVVFVSKDVAKHLGFQ", "down_seq": "AEEALRGLYGRVRKGAVLVC", "snv": [ { "evidence": [ { "id": "rs1558452514", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558452514" }, { "id": "rs1558452514", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1558452514" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099239", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S203", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777377724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777377724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777377724", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777377724#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777377724", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777377724", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs777377724", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs777377724", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GYGDVVFVSKDVAKHLGFQS", "down_seq": "EEALRGLYGRVRKGAVLVCA", "snv": [ { "evidence": [ { "id": "rs777377724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724" }, { "id": "rs777377724", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724" }, { "id": "rs777377724", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777377724#frequency_tab" }, { "id": "rs777377724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777377724" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099241", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A204", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs777377724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724" }, { "id": "rs777377724", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777377724" }, { "id": "rs777377724", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777377724#frequency_tab" }, { "id": "rs777377724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777377724" }, { "id": "rs777377724", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs777377724" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099241", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A204", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs571894321", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs571894321", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs571894321", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs571894321", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs571894321", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs571894321", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs571894321", "url": "http://gnomad.broadinstitute.org/awesome?query=rs571894321", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GDVVFVSKDVAKHLGFQSAE", "down_seq": "ALRGLYGRVRKGAVLVCAWA", "snv": [ { "evidence": [ { "id": "rs571894321", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs571894321" }, { "id": "rs571894321", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs571894321" }, { "id": "rs571894321", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs571894321" }, { "id": "rs571894321", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs571894321" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099247", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "E206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1360561772", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360561772", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360561772", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360561772#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1360561772", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360561772", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DVVFVSKDVAKHLGFQSAEE", "down_seq": "LRGLYGRVRKGAVLVCAWAE", "snv": [ { "evidence": [ { "id": "rs1360561772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360561772" }, { "id": "rs1360561772", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360561772#frequency_tab" }, { "id": "rs1360561772", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360561772" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099251", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A207", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1360561772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360561772" }, { "id": "rs1360561772", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360561772#frequency_tab" }, { "id": "rs1360561772", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360561772" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099251", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A207", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VVFVSKDVAKHLGFQSAEEA", "down_seq": "RGLYGRVRKGAVLVCAWAEE", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099255", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L208", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099253", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L208", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.189.189", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749810467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749810467", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749810467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749810467", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749810467", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749810467#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749810467", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749810467", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "", "down_seq": "DKYPKEDSEIRCLSQRWQRG", "snv": [ { "evidence": [ { "id": "rs749810467", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749810467" }, { "id": "rs749810467", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749810467" }, { "id": "rs749810467", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749810467#frequency_tab" }, { "id": "rs749810467", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749810467" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087318", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V20", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745789565", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745789565", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745789565", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745789565", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745789565", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745789565#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745789565", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745789565", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VSKDVAKHLGFQSAEEALRG", "down_seq": "YGRVRKGAVLVCAWAEEGAD", "snv": [ { "evidence": [ { "id": "rs745789565", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745789565" }, { "id": "rs745789565", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745789565" }, { "id": "rs745789565", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745789565#frequency_tab" }, { "id": "rs745789565", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745789565" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099264", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L211", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670620350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670620350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670620350", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670620350#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SKDVAKHLGFQSAEEALRGL", "down_seq": "GRVRKGAVLVCAWAEEGADA", "snv": [ { "evidence": [ { "id": "rs1670620350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670620350" }, { "id": "rs1670620350", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670620350#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099266", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y212", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779644253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779644253", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779644253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779644253", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1328514096", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328514096", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1328514096", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328514096#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1328514096", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328514096", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KDVAKHLGFQSAEEALRGLY", "down_seq": "RVRKGAVLVCAWAEEGADAL", "snv": [ { "evidence": [ { "id": "rs779644253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779644253" }, { "id": "rs779644253", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779644253" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099268", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G213", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1328514096", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1328514096" }, { "id": "rs1328514096", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1328514096#frequency_tab" }, { "id": "rs1328514096", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1328514096" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099269", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G213", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099268", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G213", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs748433617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748433617", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748433617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748433617", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748433617", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748433617#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748433617", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748433617", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs748433617", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748433617", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735561", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735561#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735561", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs61735561", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735561", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DVAKHLGFQSAEEALRGLYG", "down_seq": "VRKGAVLVCAWAEEGADALG", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs748433617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748433617" }, { "id": "rs748433617", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748433617" }, { "id": "rs748433617", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748433617#frequency_tab" }, { "id": "rs748433617", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748433617" }, { "id": "rs748433617", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748433617" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099271", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R214", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs61735561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561" }, { "id": "rs61735561", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735561" }, { "id": "rs61735561", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561" }, { "id": "rs61735561", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735561#frequency_tab" }, { "id": "rs61735561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735561" }, { "id": "rs61735561", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735561" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099272", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R214", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs61735561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561" }, { "id": "rs61735561", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735561" }, { "id": "rs61735561", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735561" }, { "id": "rs61735561", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735561#frequency_tab" }, { "id": "rs61735561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735561" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099272", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R214", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs886055889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886055889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886055889", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371146138#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs371146138", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371146138", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VAKHLGFQSAEEALRGLYGR", "down_seq": "RKGAVLVCAWAEEGADALGP", "snv": [ { "evidence": [ { "id": "rs886055889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055889" }, { "id": "rs886055889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886055889" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099274", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V215", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs371146138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" }, { "id": "rs371146138", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371146138" }, { "id": "rs371146138", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371146138#frequency_tab" }, { "id": "rs371146138", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371146138" }, { "id": "rs371146138", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371146138" }, { "id": "rs886055889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886055889" }, { "id": "rs886055889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886055889" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "NC_000002.12", "chr_pos": "27097593", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "0.000019839", "site_lbl": "V215", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1234549588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234549588", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1234549588", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1234549588#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1234549588", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234549588", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKHLGFQSAEEALRGLYGRV", "down_seq": "KGAVLVCAWAEEGADALGPD", "snv": [ { "evidence": [ { "id": "rs1234549588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234549588" }, { "id": "rs1234549588", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1234549588#frequency_tab" }, { "id": "rs1234549588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234549588" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099278", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R216", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1464106813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464106813", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1464106813", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1464106813#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767763890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767763890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767763890", "url": "https://www.ensembl.org/id/rs767763890", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KHLGFQSAEEALRGLYGRVR", "down_seq": "GAVLVCAWAEEGADALGPDG", "snv": [ { "evidence": [ { "id": "rs1464106813", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464106813" }, { "id": "rs1464106813", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1464106813#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099280", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767763890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767763890" }, { "id": "rs767763890", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs767763890" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099281", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K217", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.197.197", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs139475529", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139475529", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139475529", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139475529", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139475529", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139475529#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs139475529", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139475529", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs763164496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763164496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763164496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763164496", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763164496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763164496", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "HLGFQSAEEALRGLYGRVRK", "down_seq": "AVLVCAWAEEGADALGPDGK", "snv": [ { "evidence": [ { "id": "rs139475529", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139475529" }, { "id": "rs139475529", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139475529" }, { "id": "rs139475529", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139475529#frequency_tab" }, { "id": "rs139475529", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139475529" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099284", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G218", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763164496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763164496" }, { "id": "rs763164496", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763164496" }, { "id": "rs763164496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763164496" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099283", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G218", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761385266", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761385266", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761385266", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761385266", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LGFQSAEEALRGLYGRVRKG", "down_seq": "VLVCAWAEEGADALGPDGKL", "snv": [ { "evidence": [ { "id": "rs761385266", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266" }, { "id": "rs761385266", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266" }, { "id": "rs761385266", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761385266" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099421", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs761385266", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266" }, { "id": "rs761385266", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761385266" }, { "id": "rs761385266", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761385266" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099421", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A219", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771363247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771363247", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771363247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771363247", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771363247", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771363247#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771363247", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771363247", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1465753407", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465753407", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1465753407", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465753407", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MEEKQILCVGLVVLDVISLV", "down_seq": "KYPKEDSEIRCLSQRWQRGG", "snv": [ { "evidence": [ { "id": "rs771363247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771363247" }, { "id": "rs771363247", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771363247" }, { "id": "rs771363247", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771363247#frequency_tab" }, { "id": "rs771363247", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771363247" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087322", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D21", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087320", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D21", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1465753407", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465753407" }, { "id": "rs1465753407", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465753407" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087320", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D21", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087320", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D21", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764754040", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764754040", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764754040", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764754040", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764754040", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764754040", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GFQSAEEALRGLYGRVRKGA", "down_seq": "LVCAWAEEGADALGPDGKLL", "snv": [ { "evidence": [ { "id": "rs764754040", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764754040" }, { "id": "rs764754040", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764754040" }, { "id": "rs764754040", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764754040" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099424", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V220", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1372710291", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1372710291", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1372710291", "url": "https://www.ensembl.org/id/rs1372710291", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "FQSAEEALRGLYGRVRKGAV", "down_seq": "VCAWAEEGADALGPDGKLLH", "snv": [ { "evidence": [ { "id": "rs1372710291", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1372710291" }, { "id": "rs1372710291", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1372710291" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099428", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L221", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "QSAEEALRGLYGRVRKGAVL", "down_seq": "CAWAEEGADALGPDGKLLHS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099431", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V222", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099430", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V222", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670643677", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670643677", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670643677", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670643677#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "SAEEALRGLYGRVRKGAVLV", "down_seq": "AWAEEGADALGPDGKLLHSD", "snv": [ { "evidence": [ { "id": "rs1670643677", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670643677" }, { "id": "rs1670643677", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670643677#frequency_tab" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099435_27099445", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C223", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099434", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C223", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757902561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757902561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757902561", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757902561#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757902561", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757902561", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AEEALRGLYGRVRKGAVLVC", "down_seq": "WAEEGADALGPDGKLLHSDA", "snv": [ { "evidence": [ { "id": "rs757902561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561" }, { "id": "rs757902561", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561" }, { "id": "rs757902561", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757902561#frequency_tab" }, { "id": "rs757902561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757902561" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099436", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A224", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757902561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561" }, { "id": "rs757902561", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757902561" }, { "id": "rs757902561", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757902561#frequency_tab" }, { "id": "rs757902561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757902561" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099436", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A224", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs897749184", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs897749184", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs897749184", "url": "https://www.ensembl.org/id/rs897749184", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs980080107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs980080107", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs980080107", "url": "https://www.ncbi.nlm.nih.gov/snp/rs980080107#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs980080107", "url": "http://gnomad.broadinstitute.org/awesome?query=rs980080107", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751508802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751508802", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751508802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751508802", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751508802", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751508802#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751508802", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751508802", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "EEALRGLYGRVRKGAVLVCA", "down_seq": "AEEGADALGPDGKLLHSDAF", "snv": [ { "evidence": [ { "id": "rs897749184", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs897749184" }, { "id": "rs897749184", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs897749184" }, { "id": "rs980080107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs980080107" }, { "id": "rs980080107", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs980080107#frequency_tab" }, { "id": "rs980080107", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs980080107" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099441", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W225", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751508802", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751508802" }, { "id": "rs751508802", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751508802" }, { "id": "rs751508802", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751508802#frequency_tab" }, { "id": "rs751508802", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751508802" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099439", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W225", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.206.206", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754789918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754789918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754789918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754789918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754789918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754789918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754789918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754789918", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1670645599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670645599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670645599", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670645599#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ALRGLYGRVRKGAVLVCAWA", "down_seq": "EGADALGPDGKLLHSDAFPP", "snv": [ { "evidence": [ { "id": "rs754789918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754789918" }, { "id": "rs754789918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754789918" }, { "id": "rs754789918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754789918#frequency_tab" }, { "id": "rs754789918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754789918" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099445", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E227", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1670645599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670645599" }, { "id": "rs1670645599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670645599#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099446", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E227", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs148627840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148627840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148627840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148627840", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781078287", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781078287", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781078287", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781078287#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781078287", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781078287", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs745546639", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745546639", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LRGLYGRVRKGAVLVCAWAE", "down_seq": "GADALGPDGKLLHSDAFPPP", "snv": [ { "evidence": [ { "id": "rs148627840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148627840" }, { "id": "rs148627840", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148627840" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099450", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E228", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781078287", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287" }, { "id": "rs781078287", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287" }, { "id": "rs781078287", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781078287#frequency_tab" }, { "id": "rs781078287", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781078287" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099449", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E228", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs781078287", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287" }, { "id": "rs781078287", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781078287" }, { "id": "rs781078287", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781078287#frequency_tab" }, { "id": "rs781078287", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781078287" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099449", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E228", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745546639", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745546639" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099446AGG", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E228", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1572882180", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572882180", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572882180", "url": "https://www.ensembl.org/id/rs1572882180", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RGLYGRVRKGAVLVCAWAEE", "down_seq": "ADALGPDGKLLHSDAFPPPR", "snv": [ { "evidence": [ { "id": "rs1572882180", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572882180" }, { "id": "rs1572882180", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572882180" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099452", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G229", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774729319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774729319", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774729319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774729319", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774729319", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774729319#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774729319", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774729319", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EEKQILCVGLVVLDVISLVD", "down_seq": "YPKEDSEIRCLSQRWQRGGN", "snv": [ { "evidence": [ { "id": "rs774729319", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774729319" }, { "id": "rs774729319", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774729319" }, { "id": "rs774729319", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774729319#frequency_tab" }, { "id": "rs774729319", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774729319" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087323", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K22", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745997707", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745997707", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745997707", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745997707", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745997707", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745997707#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745997707", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745997707", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GLYGRVRKGAVLVCAWAEEG", "down_seq": "DALGPDGKLLHSDAFPPPRV", "snv": [ { "evidence": [ { "id": "rs745997707", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745997707" }, { "id": "rs745997707", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745997707" }, { "id": "rs745997707", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745997707#frequency_tab" }, { "id": "rs745997707", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745997707" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099454", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A230", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2148370955", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148370955", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2148370955", "url": "https://www.ensembl.org/id/rs2148370955", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs139948811", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139948811", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139948811", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139948811", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs139948811", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139948811", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139948811", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139948811#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs139948811", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139948811", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LYGRVRKGAVLVCAWAEEGA", "down_seq": "ALGPDGKLLHSDAFPPPRVV", "snv": [ { "evidence": [ { "id": "rs2148370955", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148370955" }, { "id": "rs2148370955", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2148370955" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099458", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D231", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs139948811", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139948811" }, { "id": "rs139948811", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139948811" }, { "id": "rs139948811", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139948811" }, { "id": "rs139948811", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139948811#frequency_tab" }, { "id": "rs139948811", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139948811" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099457", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D231", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs747489398", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747489398", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747489398", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747489398", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747489398", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747489398", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YGRVRKGAVLVCAWAEEGAD", "down_seq": "LGPDGKLLHSDAFPPPRVVD", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099460", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A232", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs747489398", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747489398" }, { "id": "rs747489398", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747489398" }, { "id": "rs747489398", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747489398" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099460", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768902999", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768902999", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768902999", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768902999", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768902999", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768902999#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768902999", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768902999", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GRVRKGAVLVCAWAEEGADA", "down_seq": "GPDGKLLHSDAFPPPRVVDT", "snv": [ { "evidence": [ { "id": "rs768902999", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768902999" }, { "id": "rs768902999", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768902999" }, { "id": "rs768902999", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768902999#frequency_tab" }, { "id": "rs768902999", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768902999" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099464", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L233", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.213.213", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RVRKGAVLVCAWAEEGADAL", "down_seq": "PDGKLLHSDAFPPPRVVDTL", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099467", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G234", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225085709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225085709", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225085709", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225085709", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VRKGAVLVCAWAEEGADALG", "down_seq": "DGKLLHSDAFPPPRVVDTLG", "snv": [ { "evidence": [ { "id": "rs1225085709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225085709" }, { "id": "rs1225085709", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225085709" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099469", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P235", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.216.216", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1490275819", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1490275819", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1490275819", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1490275819", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GAVLVCAWAEEGADALGPDG", "down_seq": "LLHSDAFPPPRVVDTLGAGD", "snv": [ { "evidence": [ { "id": "rs1490275819", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1490275819" }, { "id": "rs1490275819", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1490275819" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099478", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K238", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670648807", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670648807", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670648807", "url": "https://www.ensembl.org/id/rs1670648807", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AVLVCAWAEEGADALGPDGK", "down_seq": "LHSDAFPPPRVVDTLGAGDT", "snv": [ { "evidence": [ { "id": "rs1670648807", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670648807" }, { "id": "rs1670648807", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670648807" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099482", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L239", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746170580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746170580", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746170580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746170580", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746170580", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746170580#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746170580", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746170580", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1021946005", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021946005", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1021946005", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021946005", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1489541241", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489541241", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1489541241", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489541241", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EKQILCVGLVVLDVISLVDK", "down_seq": "PKEDSEIRCLSQRWQRGGNA", "snv": [ { "evidence": [ { "id": "rs746170580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746170580" }, { "id": "rs746170580", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746170580" }, { "id": "rs746170580", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746170580#frequency_tab" }, { "id": "rs746170580", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746170580" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087328", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y23", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1021946005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021946005" }, { "id": "rs1021946005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021946005" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087327", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y23", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1489541241", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1489541241" }, { "id": "rs1489541241", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1489541241" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087326", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y23", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs567971261", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs567971261", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs567971261", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs567971261", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs567971261", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs567971261", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs567971261", "url": "http://gnomad.broadinstitute.org/awesome?query=rs567971261", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VLVCAWAEEGADALGPDGKL", "down_seq": "HSDAFPPPRVVDTLGAGDTF", "snv": [ { "evidence": [ { "id": "rs567971261", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs567971261" }, { "id": "rs567971261", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs567971261" }, { "id": "rs567971261", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs567971261" }, { "id": "rs567971261", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs567971261" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099484", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "L240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1181776303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1181776303", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1181776303", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1181776303", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LVCAWAEEGADALGPDGKLL", "down_seq": "SDAFPPPRVVDTLGAGDTFN", "snv": [ { "evidence": [ { "id": "rs1181776303", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1181776303" }, { "id": "rs1181776303", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1181776303" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099488", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H241", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs992781636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992781636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs992781636", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992781636#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs992781636", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992781636", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs992781636", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs992781636", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VCAWAEEGADALGPDGKLLH", "down_seq": "DAFPPPRVVDTLGAGDTFNA", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs992781636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs992781636" }, { "id": "rs992781636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs992781636#frequency_tab" }, { "id": "rs992781636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs992781636" }, { "id": "rs992781636", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs992781636" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099491", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S242", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.222.222", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670650131", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670650131", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670650131", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670650131#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CAWAEEGADALGPDGKLLHS", "down_seq": "AFPPPRVVDTLGAGDTFNAS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1670650131", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670650131" }, { "id": "rs1670650131", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670650131#frequency_tab" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099493", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D243", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670650425", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670650425", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670650425", "url": "https://www.ensembl.org/id/rs1670650425", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1670650425", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670650425", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AWAEEGADALGPDGKLLHSD", "down_seq": "FPPPRVVDTLGAGDTFNASV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1670650425", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670650425" }, { "id": "rs1670650425", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670650425" }, { "id": "rs1670650425", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670650425" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099496", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A244", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1159314704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159314704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159314704", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159314704", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1159314704", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1159314704", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "WAEEGADALGPDGKLLHSDA", "down_seq": "PPPRVVDTLGAGDTFNASVI", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1159314704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159314704" }, { "id": "rs1159314704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1159314704" }, { "id": "rs1159314704", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1159314704" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099499", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F245", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368056714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368056714", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368056714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368056714", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368056714", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368056714#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368056714", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368056714", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs368056714", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368056714", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AEEGADALGPDGKLLHSDAF", "down_seq": "PPRVVDTLGAGDTFNASVIF", "snv": [ { "evidence": [ { "id": "rs368056714", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368056714" }, { "id": "rs368056714", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368056714" }, { "id": "rs368056714", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368056714#frequency_tab" }, { "id": "rs368056714", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368056714" }, { "id": "rs368056714", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs368056714" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099503", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P246", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670651727", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670651727", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670651727", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670651727#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670651727", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670651727", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EGADALGPDGKLLHSDAFPP", "down_seq": "RVVDTLGAGDTFNASVIFSL", "snv": [ { "evidence": [ { "id": "rs1670651727", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670651727" }, { "id": "rs1670651727", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670651727#frequency_tab" }, { "id": "rs1670651727", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670651727" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099509", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P248", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199989985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199989985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199989985", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199989985", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199989985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199989985", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199989985", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199989985#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199989985", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199989985", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199989985", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199989985", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs549772974", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549772974", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs549772974", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549772974", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs549772974", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549772974", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs549772974", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549772974#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs549772974", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549772974", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GADALGPDGKLLHSDAFPPP", "down_seq": "VVDTLGAGDTFNASVIFSLS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs199989985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199989985" }, { "id": "rs199989985", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199989985" }, { "id": "rs199989985", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199989985" }, { "id": "rs199989985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199989985#frequency_tab" }, { "id": "rs199989985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199989985" }, { "id": "rs199989985", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199989985" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099511", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R249", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs549772974", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549772974" }, { "id": "rs549772974", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs549772974" }, { "id": "rs549772974", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs549772974" }, { "id": "rs549772974", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs549772974#frequency_tab" }, { "id": "rs549772974", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs549772974" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099512", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R249", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099512", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R249", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1250129729", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250129729", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1250129729", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250129729", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KQILCVGLVVLDVISLVDKY", "down_seq": "KEDSEIRCLSQRWQRGGNAS", "snv": [ { "evidence": [ { "id": "rs1250129729", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1250129729" }, { "id": "rs1250129729", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1250129729" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087329", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P24", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1333441159", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333441159", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1333441159", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333441159", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs755955022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755955022", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755955022", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755955022#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755955022", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755955022", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ADALGPDGKLLHSDAFPPPR", "down_seq": "VDTLGAGDTFNASVIFSLSQ", "snv": [ { "evidence": [ { "id": "rs1333441159", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1333441159" }, { "id": "rs1333441159", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1333441159" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099515", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V250", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755955022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022" }, { "id": "rs755955022", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022" }, { "id": "rs755955022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755955022#frequency_tab" }, { "id": "rs755955022", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755955022" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099514", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V250", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755955022", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022" }, { "id": "rs755955022", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755955022" }, { "id": "rs755955022", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755955022#frequency_tab" }, { "id": "rs755955022", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755955022" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099514", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V250", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1443773312", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443773312", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443773312", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443773312", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1558453261", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558453261", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1558453261", "url": "https://www.ensembl.org/id/rs1558453261", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "DALGPDGKLLHSDAFPPPRV", "down_seq": "DTLGAGDTFNASVIFSLSQG", "snv": [ { "evidence": [ { "id": "rs1443773312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443773312" }, { "id": "rs1443773312", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443773312" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099518", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V251", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1558453261", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558453261" }, { "id": "rs1558453261", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1558453261" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099517", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V251", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.231.231", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371516742", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371516742", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371516742", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371516742", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371516742", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371516742#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371516742", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371516742", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ALGPDGKLLHSDAFPPPRVV", "down_seq": "TLGAGDTFNASVIFSLSQGR", "snv": [ { "evidence": [ { "id": "rs371516742", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371516742" }, { "id": "rs371516742", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371516742" }, { "id": "rs371516742", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371516742#frequency_tab" }, { "id": "rs371516742", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371516742" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099520", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D252", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.254.254", "start_pos": 254, "end_pos": 254, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1243388312", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243388312", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1243388312", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243388312", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1294371141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294371141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1294371141", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294371141", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GPDGKLLHSDAFPPPRVVDT", "down_seq": "GAGDTFNASVIFSLSQGRSV", "snv": [ { "evidence": [ { "id": "rs1243388312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243388312" }, { "id": "rs1243388312", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243388312" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099526", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L254", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1294371141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294371141" }, { "id": "rs1294371141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294371141" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099527", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L254", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1294371141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294371141" }, { "id": "rs1294371141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294371141" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099527", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L254", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2148371236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148371236", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2148371236", "url": "https://www.ensembl.org/id/rs2148371236", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1360665578", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360665578", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360665578", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360665578", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PDGKLLHSDAFPPPRVVDTL", "down_seq": "AGDTFNASVIFSLSQGRSVQ", "snv": [ { "evidence": [ { "id": "rs2148371236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148371236" }, { "id": "rs2148371236", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2148371236" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099530", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1360665578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360665578" }, { "id": "rs1360665578", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360665578" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099529", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G255", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1195689045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1195689045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1195689045", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1195689045", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DGKLLHSDAFPPPRVVDTLG", "down_seq": "GDTFNASVIFSLSQGRSVQE", "snv": [ { "evidence": [ { "id": "rs1195689045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1195689045" }, { "id": "rs1195689045", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1195689045" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099533", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A256", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780112409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780112409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780112409", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780112409#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780112409", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780112409", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs141220653", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141220653", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141220653", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141220653#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141220653", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141220653", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780112409", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780112409", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GKLLHSDAFPPPRVVDTLGA", "down_seq": "DTFNASVIFSLSQGRSVQEA", "snv": [ { "evidence": [ { "id": "rs780112409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409" }, { "id": "rs780112409", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409" }, { "id": "rs780112409", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780112409#frequency_tab" }, { "id": "rs780112409", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780112409" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099536", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G257", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs141220653", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141220653" }, { "id": "rs141220653", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141220653#frequency_tab" }, { "id": "rs141220653", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141220653" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099535", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G257", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs780112409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409" }, { "id": "rs780112409", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780112409" }, { "id": "rs780112409", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780112409#frequency_tab" }, { "id": "rs780112409", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780112409" }, { "id": "rs780112409", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780112409" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099536", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G257", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774520724", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774520724", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774520724", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774520724", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KLLHSDAFPPPRVVDTLGAG", "down_seq": "TFNASVIFSLSQGRSVQEAL", "snv": [ { "evidence": [ { "id": "rs774520724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774520724" }, { "id": "rs774520724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774520724" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099538", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D258", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774520724", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774520724" }, { "id": "rs774520724", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774520724" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099538", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D258", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1572882536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572882536", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572882536", "url": "https://www.ensembl.org/id/rs1572882536", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLHSDAFPPPRVVDTLGAGD", "down_seq": "FNASVIFSLSQGRSVQEALR", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099541", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T259", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1572882536", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572882536" }, { "id": "rs1572882536", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572882536" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099541", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T259", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781648272", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781648272", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781648272", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781648272", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781648272", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781648272", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HSDAFPPPRVVDTLGAGDTF", "down_seq": "ASVIFSLSQGRSVQEALRFG", "snv": [ { "evidence": [ { "id": "rs781648272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781648272" }, { "id": "rs781648272", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781648272" }, { "id": "rs781648272", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781648272" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099548", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N261", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670656739", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670656739", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670656739", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670656739#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670656739", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670656739", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SDAFPPPRVVDTLGAGDTFN", "down_seq": "SVIFSLSQGRSVQEALRFGC", "snv": [ { "evidence": [ { "id": "rs1670656739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670656739" }, { "id": "rs1670656739", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670656739#frequency_tab" }, { "id": "rs1670656739", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670656739" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099551", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A262", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.242.242", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs770138704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770138704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770138704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770138704", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770138704", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770138704", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DAFPPPRVVDTLGAGDTFNA", "down_seq": "VIFSLSQGRSVQEALRFGCQ", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099553", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S263", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs770138704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770138704" }, { "id": "rs770138704", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770138704" }, { "id": "rs770138704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770138704" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099553", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs114353144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114353144", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs114353144", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114353144", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs114353144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114353144", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs114353144", "url": "https://www.ncbi.nlm.nih.gov/snp/rs114353144#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs114353144", "url": "http://gnomad.broadinstitute.org/awesome?query=rs114353144", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs114353144", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114353144", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "AFPPPRVVDTLGAGDTFNAS", "down_seq": "IFSLSQGRSVQEALRFGCQV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs114353144", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114353144" }, { "id": "rs114353144", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114353144" }, { "id": "rs114353144", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs114353144" }, { "id": "rs114353144", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs114353144#frequency_tab" }, { "id": "rs114353144", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs114353144" }, { "id": "rs114353144", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs114353144" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099556", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V264", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773873126", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773873126", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773873126", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773873126", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773873126", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773873126#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773873126", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773873126", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FPPPRVVDTLGAGDTFNASV", "down_seq": "FSLSQGRSVQEALRFGCQVA", "snv": [ { "evidence": [ { "id": "rs773873126", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773873126" }, { "id": "rs773873126", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773873126" }, { "id": "rs773873126", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773873126#frequency_tab" }, { "id": "rs773873126", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773873126" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099559", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I265", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1052033257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1052033257", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1052033257", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1052033257#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "PRVVDTLGAGDTFNASVIFS", "down_seq": "SQGRSVQEALRFGCQVAGKK", "snv": [ { "evidence": [ { "id": "rs1052033257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1052033257" }, { "id": "rs1052033257", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1052033257#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099569", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L268", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1411651658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411651658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1411651658", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411651658", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1411651658", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1411651658", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RVVDTLGAGDTFNASVIFSL", "down_seq": "QGRSVQEALRFGCQVAGKKC", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1411651658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1411651658" }, { "id": "rs1411651658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1411651658" }, { "id": "rs1411651658", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1411651658" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099572", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S269", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs968617509", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs968617509", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs968617509", "url": "https://www.ncbi.nlm.nih.gov/snp/rs968617509#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1371873821", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371873821", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1371873821", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371873821", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ILCVGLVVLDVISLVDKYPK", "down_seq": "DSEIRCLSQRWQRGGNASNS", "snv": [ { "evidence": [ { "id": "rs968617509", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs968617509" }, { "id": "rs968617509", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs968617509#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087336", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E26", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1371873821", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1371873821" }, { "id": "rs1371873821", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1371873821" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087335", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E26", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1338230504", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338230504", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1338230504", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1338230504#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1338230504", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338230504", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202164115", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202164115", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202164115", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202164115#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202164115", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs202164115", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202164115", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VDTLGAGDTFNASVIFSLSQ", "down_seq": "RSVQEALRFGCQVAGKKCGL", "snv": [ { "evidence": [ { "id": "rs1338230504", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338230504" }, { "id": "rs1338230504", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1338230504#frequency_tab" }, { "id": "rs1338230504", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338230504" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099665", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G271", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs202164115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202164115" }, { "id": "rs202164115", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202164115" }, { "id": "rs202164115", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202164115" }, { "id": "rs202164115", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202164115#frequency_tab" }, { "id": "rs202164115", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202164115" }, { "id": "rs202164115", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202164115" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099577", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G271", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61735560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61735560", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735560", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61735560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735560", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61735560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61735560", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735560", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs575951862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575951862", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs575951862", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs575951862", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs575951862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575951862", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs575951862", "url": "https://www.ncbi.nlm.nih.gov/snp/rs575951862#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs575951862", "url": "http://gnomad.broadinstitute.org/awesome?query=rs575951862", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs543317237", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543317237", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs543317237", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs543317237", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs543317237", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543317237", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs543317237", "url": "https://www.ncbi.nlm.nih.gov/snp/rs543317237#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs543317237", "url": "http://gnomad.broadinstitute.org/awesome?query=rs543317237", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLGAGDTFNASVIFSLSQGR", "down_seq": "VQEALRFGCQVAGKKCGLQG", "snv": [ { "evidence": [ { "id": "rs61735560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735560" }, { "id": "rs61735560", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61735560" }, { "id": "rs61735560", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61735560" }, { "id": "rs61735560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61735560#frequency_tab" }, { "id": "rs61735560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61735560" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099670", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000981162", "site_lbl": "S273", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs575951862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575951862" }, { "id": "rs575951862", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs575951862" }, { "id": "rs575951862", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575951862" }, { "id": "rs575951862", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs575951862#frequency_tab" }, { "id": "rs575951862", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs575951862" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099671", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S273", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs543317237", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543317237" }, { "id": "rs543317237", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs543317237" }, { "id": "rs543317237", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543317237" }, { "id": "rs543317237", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs543317237#frequency_tab" }, { "id": "rs543317237", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs543317237" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099672", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S273", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138164728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138164728", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138164728", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138164728", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs138164728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138164728", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138164728", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138164728#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138164728", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138164728", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs138164728", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138164728", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LGAGDTFNASVIFSLSQGRS", "down_seq": "QEALRFGCQVAGKKCGLQGF", "snv": [ { "evidence": [ { "id": "rs138164728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138164728" }, { "id": "rs138164728", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138164728" }, { "id": "rs138164728", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138164728" }, { "id": "rs138164728", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138164728#frequency_tab" }, { "id": "rs138164728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138164728" }, { "id": "rs138164728", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138164728" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099673", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V274", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.254.254", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670672647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670672647", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670672647", "url": "https://www.ensembl.org/id/rs1670672647", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1283244477", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283244477", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1283244477", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283244477", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1283244477", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1283244477", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs776433978", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776433978", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776433978", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776433978", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GAGDTFNASVIFSLSQGRSV", "down_seq": "EALRFGCQVAGKKCGLQGFD", "snv": [ { "evidence": [ { "id": "rs1670672647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670672647" }, { "id": "rs1670672647", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670672647" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099676", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q275", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1283244477", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283244477" }, { "id": "rs1283244477", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283244477" }, { "id": "rs1283244477", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1283244477" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099678", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q275", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs776433978", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978" }, { "id": "rs776433978", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978" }, { "id": "rs776433978", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776433978" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q275", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776433978", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978" }, { "id": "rs776433978", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776433978" }, { "id": "rs776433978", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776433978" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099677", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q275", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761486852", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761486852", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761486852", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761486852#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761486852", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761486852", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AGDTFNASVIFSLSQGRSVQ", "down_seq": "ALRFGCQVAGKKCGLQGFDG", "snv": [ { "evidence": [ { "id": "rs761486852", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852" }, { "id": "rs761486852", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852" }, { "id": "rs761486852", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761486852#frequency_tab" }, { "id": "rs761486852", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761486852" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099679", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E276", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761486852", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852" }, { "id": "rs761486852", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761486852" }, { "id": "rs761486852", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761486852#frequency_tab" }, { "id": "rs761486852", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761486852" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099679", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E276", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766663579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766663579", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766663579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766663579", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766663579", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766663579", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GDTFNASVIFSLSQGRSVQE", "down_seq": "LRFGCQVAGKKCGLQGFDGI", "snv": [ { "evidence": [ { "id": "rs766663579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766663579" }, { "id": "rs766663579", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766663579" }, { "id": "rs766663579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766663579" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099682", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A277", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670673612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670673612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670673612", "url": "https://www.ensembl.org/id/rs1670673612", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "DTFNASVIFSLSQGRSVQEA", "down_seq": "RFGCQVAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1670673612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670673612" }, { "id": "rs1670673612", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670673612" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099686", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L278", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TFNASVIFSLSQGRSVQEAL", "down_seq": "FGCQVAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099689", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R279", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099689", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R279", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772449854", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772449854", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772449854", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772449854", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772449854", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772449854", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LCVGLVVLDVISLVDKYPKE", "down_seq": "SEIRCLSQRWQRGGNASNSC", "snv": [ { "evidence": [ { "id": "rs772449854", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772449854" }, { "id": "rs772449854", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772449854" }, { "id": "rs772449854", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772449854" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087338", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1485655131", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1485655131", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1485655131", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1485655131#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1485655131", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1485655131", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FNASVIFSLSQGRSVQEALR", "down_seq": "GCQVAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1485655131", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1485655131" }, { "id": "rs1485655131", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1485655131#frequency_tab" }, { "id": "rs1485655131", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1485655131" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099691", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F280", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs375971120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375971120", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375971120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375971120", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375971120", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375971120#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375971120", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375971120", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NASVIFSLSQGRSVQEALRF", "down_seq": "CQVAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs375971120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375971120" }, { "id": "rs375971120", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375971120" }, { "id": "rs375971120", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375971120#frequency_tab" }, { "id": "rs375971120", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375971120" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099694", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G281", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1572883217", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572883217", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572883217", "url": "https://www.ensembl.org/id/rs1572883217", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "ASVIFSLSQGRSVQEALRFG", "down_seq": "QVAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1572883217", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572883217" }, { "id": "rs1572883217", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572883217" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099697", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C282", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670674686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670674686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670674686", "url": "https://www.ensembl.org/id/rs1670674686", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs143430164", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143430164", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143430164", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143430164#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143430164", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143430164", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SVIFSLSQGRSVQEALRFGC", "down_seq": "VAGKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1670674686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670674686" }, { "id": "rs1670674686", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670674686" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099700", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q283", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143430164", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143430164" }, { "id": "rs143430164", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143430164#frequency_tab" }, { "id": "rs143430164", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143430164" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099702", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q283", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.285.285", "start_pos": 285, "end_pos": 285, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1222467402", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1222467402", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1222467402", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1222467402", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IFSLSQGRSVQEALRFGCQV", "down_seq": "GKKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1222467402", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1222467402" }, { "id": "rs1222467402", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1222467402" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099707", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A285", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs753207988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753207988", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753207988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753207988", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753207988", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753207988#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753207988", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753207988", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs753207988", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs753207988", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FSLSQGRSVQEALRFGCQVA", "down_seq": "KKCGLQGFDGIV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099710", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G286", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs753207988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753207988" }, { "id": "rs753207988", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753207988" }, { "id": "rs753207988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753207988#frequency_tab" }, { "id": "rs753207988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753207988" }, { "id": "rs753207988", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs753207988" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099709", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G286", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.288.288", "start_pos": 288, "end_pos": 288, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1443239293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443239293", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443239293", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443239293", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs756574998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756574998", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756574998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756574998", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756574998", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756574998", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LSQGRSVQEALRFGCQVAGK", "down_seq": "CGLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1443239293", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443239293" }, { "id": "rs1443239293", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443239293" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099715", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K288", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756574998", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756574998" }, { "id": "rs756574998", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756574998" }, { "id": "rs756574998", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756574998" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099716", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K288", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201037118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201037118", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201037118", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201037118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201037118", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201037118#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201037118", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201037118", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1177962254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177962254", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1177962254", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177962254", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "SQGRSVQEALRFGCQVAGKK", "down_seq": "GLQGFDGIV", "snv": [ { "evidence": [ { "id": "rs201037118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118" }, { "id": "rs201037118", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201037118" }, { "id": "rs201037118", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118" }, { "id": "rs201037118", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201037118#frequency_tab" }, { "id": "rs201037118", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201037118" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099719", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "C289", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1177962254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177962254" }, { "id": "rs1177962254", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177962254" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099718", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C289", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201037118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118" }, { "id": "rs201037118", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201037118" }, { "id": "rs201037118", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201037118" }, { "id": "rs201037118", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201037118#frequency_tab" }, { "id": "rs201037118", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201037118" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099719", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "C289", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2148326327", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148326327", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2148326327", "url": "https://www.ensembl.org/id/rs2148326327", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CVGLVVLDVISLVDKYPKED", "down_seq": "EIRCLSQRWQRGGNASNSCT", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs2148326327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148326327" }, { "id": "rs2148326327", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2148326327" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087342", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S28", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087342", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S28", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1452577405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452577405", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1452577405", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452577405#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1452577405", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452577405", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QGRSVQEALRFGCQVAGKKC", "down_seq": "LQGFDGIV", "snv": [ { "evidence": [ { "id": "rs1452577405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452577405" }, { "id": "rs1452577405", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452577405#frequency_tab" }, { "id": "rs1452577405", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452577405" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099722", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1387548575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387548575", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1387548575", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387548575", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "RSVQEALRFGCQVAGKKCGL", "down_seq": "GFDGIV", "snv": [ { "evidence": [ { "id": "rs1387548575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387548575" }, { "id": "rs1387548575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387548575" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099728", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q292", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1303018629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1303018629", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1303018629", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1303018629#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1303018629", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1303018629", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1303018629", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1303018629", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs749711671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749711671", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749711671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749711671", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749711671", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749711671#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749711671", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749711671", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SVQEALRFGCQVAGKKCGLQ", "down_seq": "FDGIV", "snv": [ { "evidence": [ { "id": "rs1303018629", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1303018629" }, { "id": "rs1303018629", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1303018629#frequency_tab" }, { "id": "rs1303018629", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1303018629" }, { "id": "rs1303018629", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1303018629" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099731", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G293", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs749711671", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749711671" }, { "id": "rs749711671", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749711671" }, { "id": "rs749711671", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749711671#frequency_tab" }, { "id": "rs749711671", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749711671" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099730", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G293", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670679490", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670679490", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670679490", "url": "https://www.ensembl.org/id/rs1670679490", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VQEALRFGCQVAGKKCGLQG", "down_seq": "DGIV", "snv": [ { "evidence": [ { "id": "rs1670679490", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670679490" }, { "id": "rs1670679490", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670679490" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099733", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F294", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EALRFGCQVAGKKCGLQGFD", "down_seq": "IV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27099740", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G296", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1316450619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316450619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1316450619", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316450619", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ALRFGCQVAGKKCGLQGFDG", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs1316450619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316450619" }, { "id": "rs1316450619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316450619" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099742", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I297", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs144351342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs144351342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs144351342", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144351342#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs144351342", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144351342", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LRFGCQVAGKKCGLQGFDGI", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs144351342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342" }, { "id": "rs144351342", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342" }, { "id": "rs144351342", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144351342#frequency_tab" }, { "id": "rs144351342", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144351342" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099745", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V298", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs144351342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342" }, { "id": "rs144351342", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144351342" }, { "id": "rs144351342", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144351342#frequency_tab" }, { "id": "rs144351342", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144351342" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27099745", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V298", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1306164778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1306164778", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1306164778", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1306164778#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VGLVVLDVISLVDKYPKEDS", "down_seq": "IRCLSQRWQRGGNASNSCTV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27087346", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E29", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1306164778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1306164778" }, { "id": "rs1306164778", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1306164778#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087344", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E29", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2465617315", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2465617315", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775071640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775071640", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775071640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775071640", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775071640", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775071640", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "GLVVLDVISLVDKYPKEDSE", "down_seq": "RCLSQRWQRGGNASNSCTVL", "snv": [ { "evidence": [ { "id": "rs2465617315", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2465617315" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087347", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I30", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775071640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775071640" }, { "id": "rs775071640", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775071640" }, { "id": "rs775071640", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775071640" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087349", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I30", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1414599342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1414599342", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1414599342", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1414599342", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVVLDVISLVDKYPKEDSEI", "down_seq": "CLSQRWQRGGNASNSCTVLS", "snv": [ { "evidence": [ { "id": "rs1414599342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1414599342" }, { "id": "rs1414599342", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1414599342" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092332", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R31", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779445833", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779445833", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779445833", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779445833", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779445833", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779445833", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "VVLDVISLVDKYPKEDSEIR", "down_seq": "LSQRWQRGGNASNSCTVLSL", "snv": [ { "evidence": [ { "id": "rs779445833", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779445833" }, { "id": "rs779445833", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779445833" }, { "id": "rs779445833", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779445833" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092333", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C32", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1002210485", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1002210485", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1002210485", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1002210485#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746381366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746381366", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746381366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746381366", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746381366", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746381366", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LDVISLVDKYPKEDSEIRCL", "down_seq": "QRWQRGGNASNSCTVLSLLG", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1002210485", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1002210485" }, { "id": "rs1002210485", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1002210485#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092339", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S34", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs746381366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746381366" }, { "id": "rs746381366", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746381366" }, { "id": "rs746381366", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746381366" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092340", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S34", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143419158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143419158", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143419158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143419158", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143419158", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143419158#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143419158", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143419158", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "DVISLVDKYPKEDSEIRCLS", "down_seq": "RWQRGGNASNSCTVLSLLGA", "snv": [ { "evidence": [ { "id": "rs143419158", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143419158" }, { "id": "rs143419158", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143419158" }, { "id": "rs143419158", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143419158#frequency_tab" }, { "id": "rs143419158", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143419158" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092343", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q35", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1272384716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272384716", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1272384716", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1272384716#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1272384716", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272384716", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VISLVDKYPKEDSEIRCLSQ", "down_seq": "WQRGGNASNSCTVLSLLGAP", "snv": [ { "evidence": [ { "id": "rs1272384716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272384716" }, { "id": "rs1272384716", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1272384716#frequency_tab" }, { "id": "rs1272384716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272384716" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092347", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R36", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs966430858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs966430858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs966430858", "url": "https://www.ncbi.nlm.nih.gov/snp/rs966430858#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs966430858", "url": "http://gnomad.broadinstitute.org/awesome?query=rs966430858", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "ISLVDKYPKEDSEIRCLSQR", "down_seq": "QRGGNASNSCTVLSLLGAPC", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092350", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W37", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs966430858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs966430858" }, { "id": "rs966430858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs966430858#frequency_tab" }, { "id": "rs966430858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs966430858" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092348", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W37", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780406699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780406699", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780406699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780406699", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780406699", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780406699#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780406699", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780406699", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1207531992", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207531992", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1207531992", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1207531992", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SLVDKYPKEDSEIRCLSQRW", "down_seq": "RGGNASNSCTVLSLLGAPCA", "snv": [ { "evidence": [ { "id": "rs780406699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780406699" }, { "id": "rs780406699", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780406699" }, { "id": "rs780406699", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780406699#frequency_tab" }, { "id": "rs780406699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780406699" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092351", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q38", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1207531992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207531992" }, { "id": "rs1207531992", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1207531992" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092353", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q38", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092352", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q38", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1034988307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1034988307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1034988307", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1034988307#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1034988307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1034988307", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200514692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514692", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200514692", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514692", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200514692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514692", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200514692", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200514692#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200514692", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200514692", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200514692", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514692", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVDKYPKEDSEIRCLSQRWQ", "down_seq": "GGNASNSCTVLSLLGAPCAF", "snv": [ { "evidence": [ { "id": "rs1034988307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1034988307" }, { "id": "rs1034988307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1034988307#frequency_tab" }, { "id": "rs1034988307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1034988307" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092354", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R39", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs200514692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514692" }, { "id": "rs200514692", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514692" }, { "id": "rs200514692", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200514692" }, { "id": "rs200514692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200514692#frequency_tab" }, { "id": "rs200514692", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200514692" }, { "id": "rs200514692", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200514692" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092355", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R39", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1332096848", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332096848", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1332096848", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332096848#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ME", "down_seq": "KQILCVGLVVLDVISLVDKY", "snv": [ { "evidence": [ { "id": "rs1332096848", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332096848" }, { "id": "rs1332096848", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332096848#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087266", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E3", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular basis of essential fructosuria: molecular cloning and mutational analysis of human ketohexokinase (fructokinase).", "journal": "Human molecular genetics", "date": "1994", "authors": "Bonthron DT, Brady N, Donaldson IA, Steinmann B", "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" }, { "database": "Reactome", "id": "R-HSA-70350", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-70350" }, { "database": "dbSNP", "id": "rs104893643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643" }, { "database": "dbSNP", "id": "rs104893644", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893644" } ], "reference": [ { "type": "PubMed", "id": "7833921", "url": "https://glygen.org/publication/PubMed/7833921" } ] } ], "crossref": [ { "id": "rs104893643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs104893643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs104893643", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104893643#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs104893643", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104893643", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "7833921", "url": "https://glygen.org/publication/PubMed/7833921", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs104893643", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104893643", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VDKYPKEDSEIRCLSQRWQR", "down_seq": "GNASNSCTVLSLLGAPCAFM", "snv": [ { "evidence": [ { "id": "rs104893643", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643" }, { "id": "rs104893643", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104893643" }, { "id": "rs104893643", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104893643#frequency_tab" }, { "id": "rs104893643", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104893643" }, { "id": "7833921", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/7833921" }, { "id": "rs104893643", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104893643" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092357", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G40", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P50053-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1473737975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1473737975", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1473737975", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1473737975", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DKYPKEDSEIRCLSQRWQRG", "down_seq": "NASNSCTVLSLLGAPCAFMG", "snv": [ { "evidence": [ { "id": "rs1473737975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1473737975" }, { "id": "rs1473737975", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1473737975" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092360", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1418153355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418153355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1418153355", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1418153355#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1418153355", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418153355", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KYPKEDSEIRCLSQRWQRGG", "down_seq": "ASNSCTVLSLLGAPCAFMGS", "snv": [ { "evidence": [ { "id": "rs1418153355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418153355" }, { "id": "rs1418153355", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1418153355#frequency_tab" }, { "id": "rs1418153355", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418153355" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092365", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766104457", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766104457", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766104457", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766104457", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KEDSEIRCLSQRWQRGGNAS", "down_seq": "SCTVLSLLGAPCAFMGSMAP", "snv": [ { "evidence": [ { "id": "rs766104457", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457" }, { "id": "rs766104457", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457" }, { "id": "rs766104457", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766104457" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092373", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N45", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766104457", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457" }, { "id": "rs766104457", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766104457" }, { "id": "rs766104457", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766104457" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092373", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N45", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670064531", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670064531", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670064531", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670064531#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670064531", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670064531", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDSEIRCLSQRWQRGGNASN", "down_seq": "CTVLSLLGAPCAFMGSMAPG", "snv": [ { "evidence": [ { "id": "rs1670064531", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670064531" }, { "id": "rs1670064531", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670064531#frequency_tab" }, { "id": "rs1670064531", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670064531" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092375", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S46", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142672179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142672179", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142672179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142672179", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142672179", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142672179", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751302589", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751302589", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751302589", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751302589", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "DSEIRCLSQRWQRGGNASNS", "down_seq": "TVLSLLGAPCAFMGSMAPGH", "snv": [ { "evidence": [ { "id": "rs142672179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142672179" }, { "id": "rs142672179", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142672179" }, { "id": "rs142672179", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142672179" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092380", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C47", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751302589", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589" }, { "id": "rs751302589", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589" }, { "id": "rs751302589", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751302589" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092379", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C47", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751302589", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589" }, { "id": "rs751302589", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751302589" }, { "id": "rs751302589", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751302589" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092379", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C47", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SEIRCLSQRWQRGGNASNSC", "down_seq": "VLSLLGAPCAFMGSMAPGHV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092382", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T48", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1363080307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363080307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1363080307", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1363080307#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1363080307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363080307", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1572862840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572862840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572862840", "url": "https://www.ensembl.org/id/rs1572862840", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RCLSQRWQRGGNASNSCTVL", "down_seq": "LLGAPCAFMGSMAPGHVADF", "snv": [ { "evidence": [ { "id": "rs1363080307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363080307" }, { "id": "rs1363080307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1363080307#frequency_tab" }, { "id": "rs1363080307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363080307" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092391", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S51", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1572862840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572862840" }, { "id": "rs1572862840", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572862840" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092390", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S51", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1363080307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1363080307" }, { "id": "rs1363080307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1363080307#frequency_tab" }, { "id": "rs1363080307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1363080307" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092391", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S51", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200431044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200431044", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200431044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200431044", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200431044", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200431044#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200431044", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200431044", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200431044", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200431044", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LSQRWQRGGNASNSCTVLSL", "down_seq": "GAPCAFMGSMAPGHVADFLV", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs200431044", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200431044" }, { "id": "rs200431044", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200431044" }, { "id": "rs200431044", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200431044#frequency_tab" }, { "id": "rs200431044", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200431044" }, { "id": "rs200431044", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200431044" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092396", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L53", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1443987824", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443987824", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443987824", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443987824", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768094453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768094453", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768094453", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768094453#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768094453", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768094453", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SQRWQRGGNASNSCTVLSLL", "down_seq": "APCAFMGSMAPGHVADFLVA", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092399", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G54", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1443987824", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443987824" }, { "id": "rs1443987824", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443987824" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092400", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G54", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768094453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768094453" }, { "id": "rs768094453", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768094453#frequency_tab" }, { "id": "rs768094453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768094453" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092399", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G54", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs973664792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs973664792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs973664792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs973664792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs973664792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs973664792", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1670067826", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670067826", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670067826", "url": "https://www.ensembl.org/id/rs1670067826", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QRWQRGGNASNSCTVLSLLG", "down_seq": "PCAFMGSMAPGHVADFLVAD", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092403", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A55", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs973664792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs973664792" }, { "id": "rs973664792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs973664792#frequency_tab" }, { "id": "rs973664792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs973664792" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092402", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A55", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs973664792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs973664792" }, { "id": "rs973664792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs973664792#frequency_tab" }, { "id": "rs973664792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs973664792" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092402", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A55", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1670067826", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670067826" }, { "id": "rs1670067826", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670067826" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092403", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A55", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1572862966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572862966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572862966", "url": "https://www.ensembl.org/id/rs1572862966", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1572862966", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1572862966", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1247393102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247393102", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1247393102", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247393102", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RWQRGGNASNSCTVLSLLGA", "down_seq": "CAFMGSMAPGHVADFLVADF", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1572862966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572862966" }, { "id": "rs1572862966", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572862966" }, { "id": "rs1572862966", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1572862966" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092406", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "P56", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1247393102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247393102" }, { "id": "rs1247393102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247393102" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092405", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P56", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1463133456", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463133456", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1463133456", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1463133456#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1463133456", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463133456", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "WQRGGNASNSCTVLSLLGAP", "down_seq": "AFMGSMAPGHVADFLVADFR", "snv": [ { "evidence": [ { "id": "rs1463133456", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1463133456" }, { "id": "rs1463133456", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1463133456#frequency_tab" }, { "id": "rs1463133456", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1463133456" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092409", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C57", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670068837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670068837", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670068837", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670068837#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QRGGNASNSCTVLSLLGAPC", "down_seq": "FMGSMAPGHVADFLVADFRR", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092412", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A58", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1670068837", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670068837" }, { "id": "rs1670068837", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670068837#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092411", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A58", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1049907312", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1049907312", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1049907312", "url": "https://www.ensembl.org/id/rs1049907312", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MEEK", "down_seq": "ILCVGLVVLDVISLVDKYPK", "snv": [ { "evidence": [ { "id": "rs1049907312", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1049907312" }, { "id": "rs1049907312", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1049907312" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087272", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q5", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670069538", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670069538", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670069538", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670069538#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670069538", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670069538", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs534398324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534398324", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs534398324", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534398324", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs534398324", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534398324", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs534398324", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534398324#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs534398324", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534398324", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "GGNASNSCTVLSLLGAPCAF", "down_seq": "GSMAPGHVADFLVADFRRRG", "snv": [ { "evidence": [ { "id": "rs1670069538", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670069538" }, { "id": "rs1670069538", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670069538#frequency_tab" }, { "id": "rs1670069538", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670069538" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092418", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M60", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs534398324", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534398324" }, { "id": "rs534398324", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534398324" }, { "id": "rs534398324", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534398324" }, { "id": "rs534398324", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534398324#frequency_tab" }, { "id": "rs534398324", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534398324" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092417", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "M60", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs747346841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747346841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747346841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747346841", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747346841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747346841", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs747346841", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs747346841", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NASNSCTVLSLLGAPCAFMG", "down_seq": "MAPGHVADFLVADFRRRGVD", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs747346841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747346841" }, { "id": "rs747346841", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747346841" }, { "id": "rs747346841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747346841" }, { "id": "rs747346841", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs747346841" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092424", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S62", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142663158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142663158", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142663158", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142663158", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs142663158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142663158", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142663158", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142663158#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142663158", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142663158", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1427672030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427672030", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1427672030", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1427672030#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1427672030", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427672030", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs555825182", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555825182", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs555825182", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555825182", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs555825182", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555825182", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs555825182", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555825182#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs555825182", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555825182", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "ASNSCTVLSLLGAPCAFMGS", "down_seq": "APGHVADFLVADFRRRGVDV", "snv": [ { "evidence": [ { "id": "rs142663158", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142663158" }, { "id": "rs142663158", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142663158" }, { "id": "rs142663158", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142663158" }, { "id": "rs142663158", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142663158#frequency_tab" }, { "id": "rs142663158", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142663158" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092428", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000784929", "site_lbl": "M63", "disease": [ { "disease_id": "DOID:0111680", "recommended_name": { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "essential fructosuria", "description": "A carbohydrate metabolic disorder characterized by elevated fructose levels in the blood and urine following ingestion of fructose and related sugars that has_material_basis_in homozygous or compound heterozygous mutation in KHK on chromosome 2p23.3." }, "synonyms": [ { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "hepatic fructokinase deficiency", "description": "" }, { "id": "DOID:0111680", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111680", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "essential fructosuria", "description": "Essential fructosuria is a rare autosomal recessive disorder of fructose metabolism caused by a deficiency of fructokinaseenzyme activity. It is characterized by elevated fructosemia and presence of fructosuria following ingestion of fructose and related sugars (sucrose, sorbitol). Essential fructosuria is clinically asymptomatic and harmless. Dietary restriction is not indicated." }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructokinase deficiency", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "fructosuria, essential", "description": "" }, { "id": "MONDO:0009252", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0009252", "name": "ketohexokinase deficiency", "description": "" }, { "id": "MIM:229800", "resource": "MIM", "url": "https://www.omim.org/entry/229800", "name": "Fructosuria", "description": "Fructosuria" } ], "unlinked_id_list": [], "evidence": [ { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" }, { "id": "0111680", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111680" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1427672030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1427672030" }, { "id": "rs1427672030", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1427672030#frequency_tab" }, { "id": "rs1427672030", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1427672030" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092427", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M63", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs555825182", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555825182" }, { "id": "rs555825182", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555825182" }, { "id": "rs555825182", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555825182" }, { "id": "rs555825182", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555825182#frequency_tab" }, { "id": "rs555825182", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555825182" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092426", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "M63", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769490106", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769490106", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769490106", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769490106", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769490106", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769490106", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs747801219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747801219", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747801219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747801219", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747801219", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747801219", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SNSCTVLSLLGAPCAFMGSM", "down_seq": "PGHVADFLVADFRRRGVDVS", "snv": [ { "evidence": [ { "id": "rs769490106", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769490106" }, { "id": "rs769490106", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769490106" }, { "id": "rs769490106", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769490106" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092430", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A64", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747801219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747801219" }, { "id": "rs747801219", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747801219" }, { "id": "rs747801219", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747801219" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092429", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A64", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772723045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772723045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772723045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772723045", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772723045", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772723045", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NSCTVLSLLGAPCAFMGSMA", "down_seq": "GHVADFLVADFRRRGVDVSQ", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092433", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P65", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs772723045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772723045" }, { "id": "rs772723045", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772723045" }, { "id": "rs772723045", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772723045" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092432", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P65", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670071704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670071704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670071704", "url": "https://www.ensembl.org/id/rs1670071704", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1670071474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670071474", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670071474", "url": "https://www.ensembl.org/id/rs1670071474", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SCTVLSLLGAPCAFMGSMAP", "down_seq": "HVADFLVADFRRRGVDVSQV", "snv": [ { "evidence": [ { "id": "rs1670071704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670071704" }, { "id": "rs1670071704", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670071704" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092436", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G66", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1670071474", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670071474" }, { "id": "rs1670071474", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670071474" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092435", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G66", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs928432932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs928432932", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs928432932", "url": "https://www.ncbi.nlm.nih.gov/snp/rs928432932#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CTVLSLLGAPCAFMGSMAPG", "down_seq": "VADFLVADFRRRGVDVSQVA", "snv": [ { "evidence": [ { "id": "rs928432932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs928432932" }, { "id": "rs928432932", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs928432932#frequency_tab" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092439", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H67", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670072501", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670072501", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670072501", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670072501#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLSLLGAPCAFMGSMAPGHV", "down_seq": "DFLVADFRRRGVDVSQVAWQ", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27092445", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A69", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1670072501", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670072501" }, { "id": "rs1670072501", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670072501#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27092445", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435135937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435135937", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435135937", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435135937", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "MEEKQ", "down_seq": "LCVGLVVLDVISLVDKYPKE", "snv": [ { "evidence": [ { "id": "rs1435135937", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435135937" }, { "id": "rs1435135937", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435135937" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087275", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I6", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757966336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757966336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757966336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757966336", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757966336", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757966336#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757966336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757966336", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SLLGAPCAFMGSMAPGHVAD", "down_seq": "LVADFRRRGVDVSQVAWQSK", "snv": [ { "evidence": [ { "id": "rs757966336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757966336" }, { "id": "rs757966336", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757966336" }, { "id": "rs757966336", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757966336#frequency_tab" }, { "id": "rs757966336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757966336" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094801", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F71", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs922525069", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs922525069", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs922525069", "url": "https://www.ncbi.nlm.nih.gov/snp/rs922525069#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs922525069", "url": "http://gnomad.broadinstitute.org/awesome?query=rs922525069", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LGAPCAFMGSMAPGHVADFL", "down_seq": "ADFRRRGVDVSQVAWQSKGD", "snv": [ { "evidence": [ { "id": "rs922525069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs922525069" }, { "id": "rs922525069", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs922525069#frequency_tab" }, { "id": "rs922525069", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs922525069" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094808", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V73", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779523527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779523527", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779523527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779523527", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779523527", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779523527", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs955166007", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955166007", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs955166007", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955166007", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GAPCAFMGSMAPGHVADFLV", "down_seq": "DFRRRGVDVSQVAWQSKGDT", "snv": [ { "evidence": [ { "id": "rs779523527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779523527" }, { "id": "rs779523527", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779523527" }, { "id": "rs779523527", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779523527" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094811", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A74", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs955166007", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955166007" }, { "id": "rs955166007", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955166007" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094810", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A74", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754808415", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754808415", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754808415", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754808415", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754808415", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754808415", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "APCAFMGSMAPGHVADFLVA", "down_seq": "FRRRGVDVSQVAWQSKGDTP", "snv": [ { "evidence": [ { "id": "rs754808415", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754808415" }, { "id": "rs754808415", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754808415" }, { "id": "rs754808415", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754808415" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094813", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1670238640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670238640", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670238640", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670238640", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1670238640", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670238640", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs201334254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201334254", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201334254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201334254", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201334254", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201334254#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201334254", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201334254", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201334254", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201334254", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AFMGSMAPGHVADFLVADFR", "down_seq": "RGVDVSQVAWQSKGDTPSSC", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094499", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R78", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs1670238640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670238640" }, { "id": "rs1670238640", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670238640" }, { "id": "rs1670238640", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1670238640" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094823", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R78", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs201334254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201334254" }, { "id": "rs201334254", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201334254" }, { "id": "rs201334254", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201334254#frequency_tab" }, { "id": "rs201334254", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201334254" }, { "id": "rs201334254", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201334254" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094822", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R78", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200630753", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200630753", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200630753", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200630753", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200630753", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200630753#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200630753", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200630753", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201669686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201669686", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201669686", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201669686#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201669686", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201669686", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201669686", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FMGSMAPGHVADFLVADFRR", "down_seq": "GVDVSQVAWQSKGDTPSSCC", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094826", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R79", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094826", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R79", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs200630753", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200630753" }, { "id": "rs200630753", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200630753" }, { "id": "rs200630753", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200630753#frequency_tab" }, { "id": "rs200630753", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200630753" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094826", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R79", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" }, { "id": "rs201669686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201669686" }, { "id": "rs201669686", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201669686" }, { "id": "rs201669686", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201669686" }, { "id": "rs201669686", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201669686#frequency_tab" }, { "id": "rs201669686", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201669686" }, { "id": "rs201669686", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201669686" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094825", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R79", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1452857250", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452857250", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1452857250", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452857250", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MEEKQI", "down_seq": "CVGLVVLDVISLVDKYPKED", "snv": [ { "evidence": [ { "id": "rs1452857250", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452857250" }, { "id": "rs1452857250", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452857250" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087279", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L7", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs957958227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs957958227", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs957958227", "url": "https://www.ensembl.org/id/rs957958227", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MGSMAPGHVADFLVADFRRR", "down_seq": "VDVSQVAWQSKGDTPSSCCI", "snv": [ { "evidence": [ { "id": "rs957958227", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs957958227" }, { "id": "rs957958227", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs957958227" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094829", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747581100", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747581100", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747581100", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747581100#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747581100", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747581100", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775231097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775231097", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775231097", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775231097", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775231097", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775231097#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775231097", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775231097", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GSMAPGHVADFLVADFRRRG", "down_seq": "DVSQVAWQSKGDTPSSCCII", "snv": [ { "evidence": [ { "id": "rs747581100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100" }, { "id": "rs747581100", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100" }, { "id": "rs747581100", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747581100#frequency_tab" }, { "id": "rs747581100", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747581100" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094832", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V81", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747581100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100" }, { "id": "rs747581100", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747581100" }, { "id": "rs747581100", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747581100#frequency_tab" }, { "id": "rs747581100", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747581100" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094832", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V81", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775231097", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775231097" }, { "id": "rs775231097", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775231097" }, { "id": "rs775231097", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775231097#frequency_tab" }, { "id": "rs775231097", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775231097" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094831", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V81", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SMAPGHVADFLVADFRRRGV", "down_seq": "VSQVAWQSKGDTPSSCCIIN", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094512", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D82", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs146252182", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146252182", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146252182", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146252182", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146252182", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146252182#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs146252182", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146252182", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MAPGHVADFLVADFRRRGVD", "down_seq": "SQVAWQSKGDTPSSCCIINN", "snv": [ { "evidence": [ { "id": "rs146252182", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146252182" }, { "id": "rs146252182", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146252182" }, { "id": "rs146252182", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146252182#frequency_tab" }, { "id": "rs146252182", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146252182" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094837", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V83", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P50053", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs562937111", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562937111", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs562937111", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562937111", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs562937111", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562937111#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs562937111", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562937111", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APGHVADFLVADFRRRGVDV", "down_seq": "QVAWQSKGDTPSSCCIINNS", "snv": [ { "evidence": [ { "id": "P50053", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P50053" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "2", "chr_pos": "27094841", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S84", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs562937111", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562937111" }, { "id": "rs562937111", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562937111" }, { "id": "rs562937111", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562937111#frequency_tab" }, { "id": "rs562937111", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562937111" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094840", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S84", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670240777", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670240777", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670240777", "url": "https://www.ensembl.org/id/rs1670240777", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PGHVADFLVADFRRRGVDVS", "down_seq": "VAWQSKGDTPSSCCIINNSN", "snv": [ { "evidence": [ { "id": "rs1670240777", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670240777" }, { "id": "rs1670240777", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670240777" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094844", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q85", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772905836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772905836", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772905836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772905836", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772905836", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772905836#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772905836", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772905836", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GHVADFLVADFRRRGVDVSQ", "down_seq": "AWQSKGDTPSSCCIINNSNG", "snv": [ { "evidence": [ { "id": "rs772905836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772905836" }, { "id": "rs772905836", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772905836" }, { "id": "rs772905836", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772905836#frequency_tab" }, { "id": "rs772905836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772905836" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094846", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V86", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs149502628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149502628", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HVADFLVADFRRRGVDVSQV", "down_seq": "WQSKGDTPSSCCIINNSNGN", "snv": [ { "evidence": [ { "id": "rs149502628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149502628" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094850", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A87", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1558446841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558446841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1558446841", "url": "https://www.ensembl.org/id/rs1558446841", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "VADFLVADFRRRGVDVSQVA", "down_seq": "QSKGDTPSSCCIINNSNGNR", "snv": [ { "evidence": [ { "id": "rs1558446841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1558446841" }, { "id": "rs1558446841", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1558446841" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094853", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W88", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1390789894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1390789894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1390789894", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1390789894", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "MEEKQIL", "down_seq": "VGLVVLDVISLVDKYPKEDS", "snv": [ { "evidence": [ { "id": "rs1390789894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1390789894" }, { "id": "rs1390789894", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1390789894" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087283", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C8", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670241697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670241697", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670241697", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670241697#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1670241697", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670241697", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1063550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1063550", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063550", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1063550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063550", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1063550", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063550#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1063550", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063550", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DFLVADFRRRGVDVSQVAWQ", "down_seq": "KGDTPSSCCIINNSNGNRTI", "snv": [ { "evidence": [ { "id": "rs1670241697", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670241697" }, { "id": "rs1670241697", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1670241697#frequency_tab" }, { "id": "rs1670241697", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1670241697" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094858", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S90", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1063550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063550" }, { "id": "rs1063550", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063550" }, { "id": "rs1063550", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063550" }, { "id": "rs1063550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063550#frequency_tab" }, { "id": "rs1063550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063550" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094859", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1222562148", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1222562148", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1222562148", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1222562148", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FLVADFRRRGVDVSQVAWQS", "down_seq": "GDTPSSCCIINNSNGNRTIV", "snv": [ { "evidence": [ { "id": "rs1222562148", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1222562148" }, { "id": "rs1222562148", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1222562148" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094862", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K91", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1471381970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471381970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1471381970", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471381970", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LVADFRRRGVDVSQVAWQSK", "down_seq": "DTPSSCCIINNSNGNRTIVL", "snv": [ { "evidence": [ { "id": "rs1471381970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471381970" }, { "id": "rs1471381970", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471381970" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094864", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G92", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P50053-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1482584405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482584405", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1482584405", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482584405", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs368277164", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368277164", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368277164", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368277164#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368277164", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368277164", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADFRRRGVDVSQVAWQSKGD", "down_seq": "PSSCCIINNSNGNRTIVLHD", "snv": [ { "evidence": [ { "id": "rs1482584405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482584405" }, { "id": "rs1482584405", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482584405" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094870", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T94", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs368277164", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164" }, { "id": "rs368277164", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164" }, { "id": "rs368277164", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368277164#frequency_tab" }, { "id": "rs368277164", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368277164" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094871", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T94", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs368277164", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164" }, { "id": "rs368277164", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368277164" }, { "id": "rs368277164", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368277164#frequency_tab" }, { "id": "rs368277164", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368277164" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094871", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T94", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1482584405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482584405" }, { "id": "rs1482584405", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1482584405" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094870", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T94", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756040787", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756040787", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756040787", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756040787#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756040787", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756040787", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1063553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063553", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1063553", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063553", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1063553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063553", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs1063553", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063553#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1063553", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063553", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs756040787", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756040787", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "RRGVDVSQVAWQSKGDTPSS", "down_seq": "CIINNSNGNRTIVLHDTSLP", "snv": [ { "evidence": [ { "id": "rs756040787", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787" }, { "id": "rs756040787", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787" }, { "id": "rs756040787", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756040787#frequency_tab" }, { "id": "rs756040787", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756040787" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094883", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C98", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1063553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063553" }, { "id": "rs1063553", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1063553" }, { "id": "rs1063553", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1063553" }, { "id": "rs1063553", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1063553#frequency_tab" }, { "id": "rs1063553", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1063553" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094884", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "C98", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs756040787", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787" }, { "id": "rs756040787", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756040787" }, { "id": "rs756040787", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756040787#frequency_tab" }, { "id": "rs756040787", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756040787" }, { "id": "rs756040787", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756040787" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094883", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C98", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1670243950", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670243950", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1670243950", "url": "https://www.ensembl.org/id/rs1670243950", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "RGVDVSQVAWQSKGDTPSSC", "down_seq": "IINNSNGNRTIVLHDTSLPD", "snv": [ { "evidence": [ { "id": "rs1670243950", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1670243950" }, { "id": "rs1670243950", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1670243950" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27094887", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C99", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P50053-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P50053-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P50053-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P50053-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P50053-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P50053-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P50053-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P50053-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P50053-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P50053-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P50053-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P50053-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P50053-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P50053-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.102.102", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P50053-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P50053-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P50053-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P50053-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P50053-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P50053-1", "length": 298, "uniprot_id": "KHK_HUMAN", "protein_name": "Ketohexokinase", "refseq_ac": "NP_000212", "refseq_name": "ketohexokinase isoform a", "gene_name": "KHK", "gene_names_uniprotkb": "KHK", "gene_names_refseq": "FRUCTU; KHK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P50053", "url": "https://www.uniprot.org/uniprotkb/P50053" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1669713839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1669713839", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1669713839", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1669713839#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1669713839", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1669713839", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MEEKQILC", "down_seq": "GLVVLDVISLVDKYPKEDSE", "snv": [ { "evidence": [ { "id": "rs1669713839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1669713839" }, { "id": "rs1669713839", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1669713839#frequency_tab" }, { "id": "rs1669713839", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1669713839" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "2", "chr_pos": "27087284", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V9", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "102", "end_pos": "102" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P50053-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P50053-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P50053-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P50053-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P50053-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P50053-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P50053-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P50053-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P50053-1.18.18", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P50053-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P50053-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P50053-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P50053-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P50053-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P50053-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P50053-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P50053-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P50053-1.29.29", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1596762866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596762866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596762866", "url": "https://www.ensembl.org/id/rs1596762866", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EAGGAEQKAASGCERLQGPP", "down_seq": "PAGKETEGSLSDSDFKEPPS", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr237", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1596762866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596762866" }, { "id": "rs1596762866", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596762866" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "16", "chr_pos": "54933130", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T237", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs903789308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903789308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs903789308", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs903789308", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs903789308", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903789308", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YTNYGSFGHLHGHPGPGPGP", "down_seq": "TGPGSHFNGLNQTVLNRADA", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr432", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs903789308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903789308" }, { "id": "rs903789308", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs903789308" }, { "id": "rs903789308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903789308" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "16", "chr_pos": "54933716", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T432", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->K).", "chr_id": "16", "chr_pos": "54933716", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T432", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78411-1.413.413", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GSPYDHTPGMAGSLGYHPYA", "down_seq": "PLGSYPYGDPAYRKNATRDA", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "54932559", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A104", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P78411-1.117.117", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGYHPYAAPLGSYPYGDPAY", "down_seq": "KNATRDATATLKAWLNEHRK", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "16", "chr_pos": "54932598", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R117", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P78411-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78411-1.136.136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YRKNATRDATATLKAWLNEH", "down_seq": "KNPYPTKGEKIMLAIITKMT", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "16", "chr_pos": "54932655", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R136", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78411-1.117.117", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "LTQVSTWFANARRRLKKENK", "down_seq": "TWTPRNRSEDEEEEENIDLE", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "M", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKM->NKT).", "chr_id": "16", "chr_pos": "54932778", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M177", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P78411-1.182.182", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TWFANARRRLKKENKMTWTP", "down_seq": "NRSEDEEEEENIDLEKNDED", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "16", "chr_pos": "54932793", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R182", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P78411-1.177.177", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.413.413", "start_pos": 413, "end_pos": 413, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PGGTVLSRPLYYTAPFYPGY", "down_seq": "NYGSFGHLHGHPGPGPGPTT", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "54933659", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T413", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P78411-1.432.432", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.470.470", "start_pos": 470, "end_pos": 470, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ADALAKDPKMLRSQSQLDLC", "down_seq": "DSPYELKKGMSDI", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "16", "chr_pos": "54933831", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K470", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P78411-1.464.464", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78411", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PSPGYNSHLQYGADPAAAAA", "down_seq": "AFSSYVGSPYDHTPGMAGSL", "snv": [ { "evidence": [ { "id": "P78411", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78411" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "54931427", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A77", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78411-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" }, { "database": "iPTMnet", "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPPSEGRLDALQGPPRTGGP", "down_seq": "PAGPAAARLAEDPAPHYPAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411" } ], "site_lbl": "Ser274" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78411-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "P78411-1", "length": 483, "uniprot_id": "IRX5_HUMAN", "protein_name": "Iroquois-class homeodomain protein IRX-5", "refseq_ac": "NP_001239126", "refseq_name": "iroquois-class homeodomain protein IRX-5 isoform 2", "gene_name": "IRX5", "gene_names_uniprotkb": "IRX5; IRX2A; IRXB2", "gene_names_refseq": "HMMS; IRX-2a; IRX5; IRXB2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" }, { "database": "iPTMnet", "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QTVLNRADALAKDPKMLRSQ", "down_seq": "QLDLCKDSPYELKKGMSDI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P78411", "url": "https://www.uniprot.org/uniprotkb/P78411" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "P78411", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P78411" } ], "site_lbl": "Ser464" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "432", "end_pos": "432" } ] }, { "type": "snv", "site_list": [ { "start_pos": "104", "end_pos": "104" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "77", "end_pos": "77" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "464", "end_pos": "464" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P78411-1.470.470", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.1045.1045", "start_pos": 1045, "end_pos": 1045, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GNPIKEITDKIIDLVSKRDG", "down_seq": "SSLIAAVAEVRVQRRPLKNR", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DGNSSLIAAVAEVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1045", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1045", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P78504-1.1047.1047", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78504-1.1064.1064", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.1064.1064", "start_pos": 1064, "end_pos": 1064, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GNSSLIAAVAEVRVQRRPLK", "down_seq": "RTDFLVPLLSSVLTVAWICC", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1064", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78504-1.1045.1045", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P78504-1.1047.1047", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.1066.1066", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2514531141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514531141", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PFSFAWPRSYTLLVEAWDSS", "down_seq": "DTVQPDSIIEKASHSGMINP", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn143", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2514531141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514531141" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->IDT).", "chr_id": "20", "chr_pos": "10663974", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P78504-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P78504-1.163.163", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "4CBZ", "url": "https://www.rcsb.org/structure/4CBZ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CC0", "url": "https://www.rcsb.org/structure/4CC0", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CC1", "url": "https://www.rcsb.org/structure/4CC1", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CBZ|B|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CBZ|A|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC0|B|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC0|A|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC1|B|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC1|A|217", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs2514526448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514526448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2067393241", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067393241", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2067393241", "url": "https://www.ensembl.org/id/rs2067393241", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2514526446", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514526446", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1131691963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1131691963", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NKFCRPRDDFFGHYACDQNG", "down_seq": "KTCMEGWMGPECNRAICRQG", "glycosylation": [ { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DDFFGHYACDQNGnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DDFFGHYACDQNGnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DDFFGHYACDQNGnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DDFFGHYACDQNGNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=4CBZ&bu=0&command=select+.B:217;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn217", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "4CBZ", "database": "PDB", "url": "https://www.rcsb.org/structure/4CBZ" }, { "id": "4CC0", "database": "PDB", "url": "https://www.rcsb.org/structure/4CC0" }, { "id": "4CC1", "database": "PDB", "url": "https://www.rcsb.org/structure/4CC1" } ] } ], "snv": [ { "evidence": [ { "id": "rs2514526448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514526448" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NKT->SKT); n-glyco-sequon-gain (NGN->NGS).", "chr_id": "20", "chr_pos": "10658512", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKT->TKT); n-glyco-sequon-gain (NGN->NGT).", "chr_id": "20", "chr_pos": "10658512", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N217", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2067393241", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067393241" }, { "id": "rs2067393241", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2067393241" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->HKT).", "chr_id": "20", "chr_pos": "10658513", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2514526446", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514526446" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->KKT).", "chr_id": "20", "chr_pos": "10658511", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1131691963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1131691963" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->XKT).", "chr_id": "20", "chr_pos": "10658514", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P78504-1.207.207", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P78504-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "4CBZ", "url": "https://www.rcsb.org/structure/4CBZ", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CC0", "url": "https://www.rcsb.org/structure/4CC0", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CC1", "url": "https://www.rcsb.org/structure/4CC1", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4CBZ|A|311", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC0|A|311", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "4CC1|A|311", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs373848497", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373848497", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373848497", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373848497", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373848497", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373848497#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373848497", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373848497", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1555829037", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555829037", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QLCDKDLNYCGTHQPCLNGG", "down_seq": "CSNTGPDKYQCSCPEGYSGP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=4CBZ&bu=0&command=select+.A:311;+center+selection;+zoom+selection" }, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr311", "evidence": [ { "id": "4CBZ", "database": "PDB", "url": "https://www.rcsb.org/structure/4CBZ" }, { "id": "4CC0", "database": "PDB", "url": "https://www.rcsb.org/structure/4CC0" }, { "id": "4CC1", "database": "PDB", "url": "https://www.rcsb.org/structure/4CC1" } ] } ], "snv": [ { "evidence": [ { "id": "rs373848497", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373848497" }, { "id": "rs373848497", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373848497" }, { "id": "rs373848497", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373848497#frequency_tab" }, { "id": "rs373848497", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373848497" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "20", "chr_pos": "10652206", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T311", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1555829037", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555829037" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->X).", "chr_id": "20", "chr_pos": "10652205", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T311", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SCKETSLGFECECSPGWTGP", "down_seq": "CSTNIDDCSPNNCSHGGTCQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr370", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "20", "chr_pos": "10651592", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T370", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P78504-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P78504-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P78504-1.384.384", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2067337017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067337017", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2067337017", "url": "https://www.ensembl.org/id/rs2067337017", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CSPGWTGPTCSTNIDDCSPN", "down_seq": "CSHGGTCQDLVNGFKCVCPP", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn382", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2067337017", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067337017" }, { "id": "rs2067337017", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2067337017" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCS->ICS).", "chr_id": "20", "chr_pos": "10650336", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N382", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P78504-1.370.370", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.384.384", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.559.559", "start_pos": 559, "end_pos": 559, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QCYNRASDYFCKCPEDYEGK", "down_seq": "CSHLKDHCRTTPCEVIDSCT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn559", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P78504-1.565.565", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.745.745", "start_pos": 745, "end_pos": 745, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1314917198", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314917198", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1314917198", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1314917198#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1314917198", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314917198", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DAFKCMCPGGWEGTTCNIAR", "down_seq": "SSCLPNPCHNGGTCVVNGES", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn745", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1314917198", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314917198" }, { "id": "rs1314917198", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1314917198#frequency_tab" }, { "id": "rs1314917198", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314917198" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->TSS).", "chr_id": "20", "chr_pos": "10644973", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N745", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P78504-1.744.744", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P78504-1.746.746", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.752.752", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.86.110", "start_pos": 86, "end_pos": 110, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "VTAGGPCSFGSGSTPVIGGNTFNLK", "start_aa": "V", "up_seq": "CTRDECDTYFKVCLKEYQSR", "down_seq": "ASRGNDRNRIVLPFSFAWPR", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VTAGGPCSFGSGSTPVIGGNTFNLK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Val", "end_aa": "Lys", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "upstream", "id": "P78504-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P78504-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.960.960", "start_pos": 960, "end_pos": 960, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2122596406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122596406", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2122596406", "url": "https://www.ensembl.org/id/rs2122596406", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SLQPVKTKCTSDSYYQDNCA", "down_seq": "ITFTFNKEMMSPGLTTEHIC", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn960", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2122596406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122596406" }, { "id": "rs2122596406", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2122596406" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->SIT).", "chr_id": "20", "chr_pos": "10641497", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N960", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P78504-1.959.959", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.962.962", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.991.991", "start_pos": 991, "end_pos": 991, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2514508419", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514508419", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SPGLTTEHICSELRNLNILK", "down_seq": "VSAEYSIYIACEPSPSANNE", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn991", "evidence": [ { "id": "P78504", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P78504#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2514508419", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514508419" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->TVS).", "chr_id": "20", "chr_pos": "10641189", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N991", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P78504-1.987.987", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.993.993", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A conserved face of the Jagged/Serrate DSL domain is involved in Notch trans-activation and cis-inhibition.", "journal": "Nature structural & molecular biology", "date": "2008", "authors": "Cordle J, Johnson S, Tay JZ, Roversi P, Wilkin MB, de Madrid BH, Shimizu H, Jensen S, Whiteman P, Jin B, Redfield C, Baron M, Lea SM, Handford PA", "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "reference": [ { "type": "PubMed", "id": "18660822", "url": "https://glygen.org/publication/PubMed/18660822" } ] } ], "crossref": [ { "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18660822", "url": "https://glygen.org/publication/PubMed/18660822", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "CDDYYYGFGCNKFCRPRDDF", "down_seq": "GHYACDQNGNKTCMEGWMGP", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Strongly reduced NOTCH1 binding.", "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" }, { "database": "PubMed", "id": "18660822", "url": "https://glygen.org/publication/PubMed/18660822" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P78504-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P78504-1.219.219", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P78504-1.1047.1047", "start_pos": 1047, "end_pos": 1047, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs267605834", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs267605834", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs267605834", "url": "http://gnomad.broadinstitute.org/awesome?query=rs267605834", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1600178441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600178441", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600178441", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1600178441#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PIKEITDKIIDLVSKRDGNS", "down_seq": "LIAAVAEVRVQRRPLKNRTD", "snv": [ { "evidence": [ { "id": "rs267605834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834" }, { "id": "rs267605834", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834" }, { "id": "rs267605834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs267605834" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NS*).", "chr_id": "20", "chr_pos": "10640842", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1047", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs267605834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834" }, { "id": "rs267605834", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs267605834" }, { "id": "rs267605834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs267605834" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSL).", "chr_id": "20", "chr_pos": "10640842", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1047", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1600178441", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600178441" }, { "id": "rs1600178441", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1600178441#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSP).", "chr_id": "20", "chr_pos": "10640843", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1047", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P78504-1.1045.1045", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P78504-1.1064.1064", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78504-1.1066.1066", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1066.1066", "start_pos": 1066, "end_pos": 1066, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2067265104", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067265104", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSLIAAVAEVRVQRRPLKNR", "down_seq": "DFLVPLLSSVLTVAWICCLV", "snv": [ { "evidence": [ { "id": "rs2067265104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067265104" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRT->NRX).", "chr_id": "20", "chr_pos": "10640783_10640787", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1066", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78504-1.1047.1047", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.1064.1064", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1101.1101", "start_pos": 1101, "end_pos": 1101, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs377617900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377617900", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377617900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377617900", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377617900", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377617900#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377617900", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377617900", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WICCLVTAFYWCLRKRRKPG", "down_seq": "HTHSASEDNTTNNVREQLNQ", "snv": [ { "evidence": [ { "id": "rs377617900", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377617900" }, { "id": "rs377617900", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377617900" }, { "id": "rs377617900", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377617900#frequency_tab" }, { "id": "rs377617900", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377617900" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SHT->NHT).", "chr_id": "20", "chr_pos": "10639853", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1101", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P78504-1.1103.1103", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78504-1.1109.1109", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1103.1103", "start_pos": 1103, "end_pos": 1103, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1555827516", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555827516", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555827516", "url": "https://www.ensembl.org/id/rs1555827516", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CCLVTAFYWCLRKRRKPGSH", "down_seq": "HSASEDNTTNNVREQLNQIK", "snv": [ { "evidence": [ { "id": "rs1555827516", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555827516" }, { "id": "rs1555827516", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1555827516" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (THS->NHS).", "chr_id": "20", "chr_pos": "10639846_10639847delin", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1103", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P78504-1.1101.1101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P78504-1.1109.1109", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1109.1109", "start_pos": 1109, "end_pos": 1109, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1044765003", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1044765003", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1044765003", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1044765003", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FYWCLRKRRKPGSHTHSASE", "down_seq": "NTTNNVREQLNQIKNPIEKH", "snv": [ { "evidence": [ { "id": "rs1044765003", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1044765003" }, { "id": "rs1044765003", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1044765003" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNT->NNT).", "chr_id": "20", "chr_pos": "10639830", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1109", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P78504-1.1101.1101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P78504-1.1103.1103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GPCSFGSGSTPVIGGNTFNL", "down_seq": "ASRGNDRNRIVLPFSFAWPR", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "20", "chr_pos": "10672758", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K110", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 0, "direction": "downstream", "id": "P78504-1.86.110", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P78504-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1142.1142", "start_pos": 1142, "end_pos": 1142, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200649621", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200649621", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200649621", "url": "https://www.ensembl.org/id/rs200649621", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IKNPIEKHGANTVPIKDYEN", "down_seq": "NSKMSKIRTHNSEVEEDDMD", "snv": [ { "evidence": [ { "id": "rs200649621", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200649621" }, { "id": "rs200649621", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200649621" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KNS->NNS).", "chr_id": "20", "chr_pos": "10639729", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1142", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P78504-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P78504-1.1160.1160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1143.1143", "start_pos": 1143, "end_pos": 1143, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1289637634", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289637634", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1289637634", "url": "https://www.ensembl.org/id/rs1289637634", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KNPIEKHGANTVPIKDYENK", "down_seq": "SKMSKIRTHNSEVEEDDMDK", "snv": [ { "evidence": [ { "id": "rs1289637634", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289637634" }, { "id": "rs1289637634", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1289637634" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKT).", "chr_id": "20", "chr_pos": "10639727", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P78504-1.1142.1142", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P78504-1.1160.1160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.1160.1160", "start_pos": 1160, "end_pos": 1160, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ENKNSKMSKIRTHNSEVEED", "down_seq": "MDKHQQKARFAKQPAYTLVD", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10639677", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1160", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P78504-1.1142.1142", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P78504-1.1143.1143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752608779", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608779", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752608779", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608779", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752608779", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752608779#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752608779", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752608779", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GSTPVIGGNTFNLKASRGND", "down_seq": "NRIVLPFSFAWPRSYTLLVE", "snv": [ { "evidence": [ { "id": "rs752608779", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608779" }, { "id": "rs752608779", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608779" }, { "id": "rs752608779", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752608779#frequency_tab" }, { "id": "rs752608779", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752608779" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDR->NDC).", "chr_id": "20", "chr_pos": "10672739", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R117", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P78504-1.86.110", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P78504-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P78504-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514537675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514537675", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PVIGGNTFNLKASRGNDRNR", "down_seq": "VLPFSFAWPRSYTLLVEAWD", "snv": [ { "evidence": [ { "id": "rs2514537675", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514537675" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRI->NRT).", "chr_id": "20", "chr_pos": "10672729", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I120", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P78504-1.86.110", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P78504-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P78504-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P78504-1.140.140", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1456733889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456733889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1456733889", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456733889#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1456733889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456733889", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IVLPFSFAWPRSYTLLVEAW", "down_seq": "SSNDTVQPDSIIEKASHSGM", "snv": [ { "evidence": [ { "id": "rs1456733889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456733889" }, { "id": "rs1456733889", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456733889#frequency_tab" }, { "id": "rs1456733889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456733889" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "20", "chr_pos": "10663984", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D140", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] }, { "disease_id": "DOID:6419", "recommended_name": { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "tetralogy of Fallot", "description": "" }, "synonyms": [ { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "Ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy." }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "Fallot tetralogy", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "TOF", "description": "" }, { "id": "MIM:187500", "resource": "MIM", "url": "https://www.omim.org/entry/187500", "name": "Tetralogy of Fallot", "description": "Tetralogy of Fallot" } ], "unlinked_id_list": [], "evidence": [ { "id": "6419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:6419" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P78504-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P78504-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P78504-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771903802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771903802", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771903802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771903802", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771903802", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771903802", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SFAWPRSYTLLVEAWDSSND", "down_seq": "VQPDSIIEKASHSGMINPSR", "snv": [ { "evidence": [ { "id": "rs771903802", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771903802" }, { "id": "rs771903802", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771903802" }, { "id": "rs771903802", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771903802" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->NDA).", "chr_id": "20", "chr_pos": "10663969", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NDT->NDI).", "chr_id": "20", "chr_pos": "10663968", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T145", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P78504-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P78504-1.163.163", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555829676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555829676", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555829676", "url": "https://www.ensembl.org/id/rs1555829676", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2067394475", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067394475", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2067394475", "url": "https://www.ensembl.org/id/rs2067394475", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NDTVQPDSIIEKASHSGMIN", "down_seq": "SRQWQTLKQNTGVAHFEYQI", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NHS).", "chr_id": "20", "chr_pos": "10658674", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P163", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1555829676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555829676" }, { "id": "rs1555829676", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1555829676" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NRS).", "chr_id": "20", "chr_pos": "10658674", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P163", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2067394475", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067394475" }, { "id": "rs2067394475", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2067394475" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "20", "chr_pos": "10658675", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P163", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P78504-1.143.143", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P78504-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P78504-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SHSGMINPSRQWQTLKQNTG", "down_seq": "AHFEYQIRVTCDDYYYGFGC", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10658636", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V176", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P78504-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78504-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SRQWQTLKQNTGVAHFEYQI", "down_seq": "VTCDDYYYGFGCNKFCRPRD", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10658611", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R184", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P78504-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370743646", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370743646", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370743646", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370743646", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370743646", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370743646#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2122623531", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122623531", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FCRPRDDFFGHYACDQNGNK", "down_seq": "CMEGWMGPECNRAICRQGCS", "snv": [ { "evidence": [ { "id": "rs370743646", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370743646" }, { "id": "rs370743646", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370743646" }, { "id": "rs370743646", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370743646#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKI).", "chr_id": "20", "chr_pos": "10658506", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2122623531", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122623531" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKX).", "chr_id": "20", "chr_pos": "10658510", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T219", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P78504-1.207.207", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P78504-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GHYACDQNGNKTCMEGWMGP", "down_seq": "CNRAICRQGCSPKHGSCKLP", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "20", "chr_pos": "10658480", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E228", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P78504-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P78504-1.219.219", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs939526863", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939526863", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs939526863", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939526863#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GSCKLPGDCRCQYGWQGLYC", "down_seq": "KCIPHPGCVHGICNEPWQCL", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs939526863", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939526863" }, { "id": "rs939526863", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939526863#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DKC->NKC).", "chr_id": "20", "chr_pos": "10652567", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D263", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P78504-1.272.272", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RCQYGWQGLYCDKCIPHPGC", "down_seq": "HGICNEPWQCLCETNWGGQL", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "20", "chr_pos": "10652540", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V272", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P78504-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514520747", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514520747", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NCEIAEHACLSDPCHNRGSC", "down_seq": "ETSLGFECECSPGWTGPTCS", "snv": [ { "evidence": [ { "id": "rs2514520747", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514520747" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KET->NET).", "chr_id": "20", "chr_pos": "10651645", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K352", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] }, { "disease_id": "DOID:6419", "recommended_name": { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "tetralogy of Fallot", "description": "" }, "synonyms": [ { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "Ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy." }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "Fallot tetralogy", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "TOF", "description": "" }, { "id": "MIM:187500", "resource": "MIM", "url": "https://www.omim.org/entry/187500", "name": "Tetralogy of Fallot", "description": "Tetralogy of Fallot" } ], "unlinked_id_list": [], "evidence": [ { "id": "6419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:6419" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P78504-1.370.370", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs753542537", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753542537", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753542537", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753542537", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753542537", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753542537", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PGWTGPTCSTNIDDCSPNNC", "down_seq": "HGGTCQDLVNGFKCVCPPQW", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCS->NCF).", "chr_id": "20", "chr_pos": "10650330", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S384", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs753542537", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753542537" }, { "id": "rs753542537", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753542537" }, { "id": "rs753542537", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753542537" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCS->NCY).", "chr_id": "20", "chr_pos": "10650330", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S384", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P78504-1.370.370", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.382.382", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2067508041", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067508041", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2067508041", "url": "https://www.ensembl.org/id/rs2067508041", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ALLCALRAKVCGASGQFELE", "down_seq": "LSMQNVNGELQNGNCCGGAR", "snv": [ { "evidence": [ { "id": "rs2067508041", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067508041" }, { "id": "rs2067508041", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2067508041" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (ILS->NLS).", "chr_id": "20", "chr_pos": "10672972", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I39", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.408.408", "start_pos": 408, "end_pos": 408, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TCQDLVNGFKCVCPPQWTGK", "down_seq": "CQLDANECEAKPCVNAKSCK", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10650258", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T408", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.452.452", "start_pos": 452, "end_pos": 452, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371635072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371635072", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371635072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371635072", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371635072", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371635072", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ASYYCDCLPGWMGQNCDINI", "down_seq": "DCLGQCQNDASCRDLVNGYR", "snv": [ { "evidence": [ { "id": "rs371635072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371635072" }, { "id": "rs371635072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371635072" }, { "id": "rs371635072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371635072" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIN->NIS).", "chr_id": "20", "chr_pos": "10649101", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N452", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "P78504-1.462.462", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78504-1.471.471", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201667840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201667840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201667840", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201667840", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201667840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201667840", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201667840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201667840", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "WMGQNCDININDCLGQCQND", "down_seq": "SCRDLVNGYRCICPPGYAGD", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs201667840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201667840" }, { "id": "rs201667840", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201667840" }, { "id": "rs201667840", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201667840" }, { "id": "rs201667840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201667840" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDA->NDT).", "chr_id": "20", "chr_pos": "10649072", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A462", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P78504-1.452.452", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P78504-1.471.471", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P78504-1.482.482", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.471.471", "start_pos": 471, "end_pos": 471, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225360203", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225360203", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225360203", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225360203", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "INDCLGQCQNDASCRDLVNG", "down_seq": "RCICPPGYAGDHCERDIDEC", "snv": [ { "evidence": [ { "id": "rs1225360203", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225360203" }, { "id": "rs1225360203", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225360203" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGY->NGC).", "chr_id": "20", "chr_pos": "10648706", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y471", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78504-1.452.452", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P78504-1.462.462", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P78504-1.482.482", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P78504-1.489.489", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.482.482", "start_pos": 482, "end_pos": 482, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs766370717", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766370717", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766370717", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766370717", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766370717", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766370717", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ASCRDLVNGYRCICPPGYAG", "down_seq": "HCERDIDECASNPCLNGGHC", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs766370717", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766370717" }, { "id": "rs766370717", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766370717" }, { "id": "rs766370717", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766370717" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DHC->NHC).", "chr_id": "20", "chr_pos": "10648674", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D482", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] }, { "disease_id": "DOID:6419", "recommended_name": { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "tetralogy of Fallot", "description": "" }, "synonyms": [ { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "Ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy." }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "Fallot tetralogy", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "TOF", "description": "" }, { "id": "MIM:187500", "resource": "MIM", "url": "https://www.omim.org/entry/187500", "name": "Tetralogy of Fallot", "description": "Tetralogy of Fallot" } ], "unlinked_id_list": [], "evidence": [ { "id": "6419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:6419" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P78504-1.462.462", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P78504-1.471.471", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P78504-1.500.500", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370107709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370107709", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370107709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370107709", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370107709", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370107709#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370107709", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370107709", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NGYRCICPPGYAGDHCERDI", "down_seq": "ECASNPCLNGGHCQNEINRF", "snv": [ { "evidence": [ { "id": "rs370107709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370107709" }, { "id": "rs370107709", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370107709" }, { "id": "rs370107709", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370107709#frequency_tab" }, { "id": "rs370107709", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370107709" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DEC->NEC).", "chr_id": "20", "chr_pos": "10648653", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D489", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] }, { "disease_id": "DOID:6419", "recommended_name": { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "tetralogy of Fallot", "description": "" }, "synonyms": [ { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "Ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy." }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "Fallot tetralogy", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "TOF", "description": "" }, { "id": "MIM:187500", "resource": "MIM", "url": "https://www.omim.org/entry/187500", "name": "Tetralogy of Fallot", "description": "Tetralogy of Fallot" } ], "unlinked_id_list": [], "evidence": [ { "id": "6419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:6419" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P78504-1.471.471", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P78504-1.482.482", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P78504-1.500.500", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P78504-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78504-1.508.508", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.500.500", "start_pos": 500, "end_pos": 500, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1600183783", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600183783", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600183783", "url": "https://www.ensembl.org/id/rs1600183783", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AGDHCERDIDECASNPCLNG", "down_seq": "HCQNEINRFQCLCPTGFSGN", "snv": [ { "evidence": [ { "id": "rs1600183783", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600183783" }, { "id": "rs1600183783", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600183783" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGG->NGS).", "chr_id": "20", "chr_pos": "10648620", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G500", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P78504-1.482.482", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P78504-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P78504-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78504-1.508.508", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514517173", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514517173", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RDIDECASNPCLNGGHCQNE", "down_seq": "NRFQCLCPTGFSGNLCQLDI", "snv": [ { "evidence": [ { "id": "rs2514517173", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514517173" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEI->NES).", "chr_id": "20", "chr_pos": "10648601", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I506", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P78504-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P78504-1.500.500", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.508.508", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IDECASNPCLNGGHCQNEIN", "down_seq": "FQCLCPTGFSGNLCQLDIDY", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10648595", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R508", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78504-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P78504-1.500.500", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P78504-1.527.527", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.527.527", "start_pos": 527, "end_pos": 527, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs934594487", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs934594487", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs934594487", "url": "https://www.ncbi.nlm.nih.gov/snp/rs934594487#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs934594487", "url": "http://gnomad.broadinstitute.org/awesome?query=rs934594487", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NRFQCLCPTGFSGNLCQLDI", "down_seq": "YCEPNPCQNGAQCYNRASDY", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs934594487", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs934594487" }, { "id": "rs934594487", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs934594487#frequency_tab" }, { "id": "rs934594487", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs934594487" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DYC->NYC).", "chr_id": "20", "chr_pos": "10648101", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D527", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P78504-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P78504-1.533.533", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P78504-1.538.538", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.533.533", "start_pos": 533, "end_pos": 533, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1365537514", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365537514", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1365537514", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1365537514#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CPTGFSGNLCQLDIDYCEPN", "down_seq": "CQNGAQCYNRASDYFCKCPE", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPC->NLC).", "chr_id": "20", "chr_pos": "10648082", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P533", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1365537514", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365537514" }, { "id": "rs1365537514", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1365537514#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NSC).", "chr_id": "20", "chr_pos": "10648083", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P533", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P78504-1.527.527", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P78504-1.538.538", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.538.538", "start_pos": 538, "end_pos": 538, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2067321510", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067321510", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2067321510", "url": "https://www.ensembl.org/id/rs2067321510", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SGNLCQLDIDYCEPNPCQNG", "down_seq": "QCYNRASDYFCKCPEDYEGK", "snv": [ { "evidence": [ { "id": "rs2067321510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2067321510" }, { "id": "rs2067321510", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2067321510" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "20", "chr_pos": "10648068", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A538", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "20", "chr_pos": "10648068", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A538", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P78504-1.527.527", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P78504-1.533.533", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.565.565", "start_pos": 565, "end_pos": 565, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514516564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514516564", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SDYFCKCPEDYEGKNCSHLK", "down_seq": "HCRTTPCEVIDSCTVAMASN", "snv": [ { "evidence": [ { "id": "rs2514516564", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514516564" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHC->NHC).", "chr_id": "20", "chr_pos": "10647987", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D565", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P78504-1.559.559", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.620.620", "start_pos": 620, "end_pos": 620, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2039238151", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2039238151", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2039238151", "url": "https://www.ensembl.org/id/rs2039238151", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GPHGKCKSQSGGKFTCDCNK", "down_seq": "FTGTYCHENINDCESNPCRN", "snv": [ { "evidence": [ { "id": "rs2039238151", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2039238151" }, { "id": "rs2039238151", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2039238151" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKG->NKS).", "chr_id": "20", "chr_pos": "10646966", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G620", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.646.646", "start_pos": 646, "end_pos": 646, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CHENINDCESNPCRNGGTCI", "down_seq": "GVNSYKCICSDGWEGAYCET", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "20", "chr_pos": "10646034", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D646", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754095380", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754095380", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754095380", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754095380", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754095380", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754095380", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VNGELQNGNCCGGARNPGDR", "down_seq": "CTRDECDTYFKVCLKEYQSR", "snv": [ { "evidence": [ { "id": "rs754095380", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754095380" }, { "id": "rs754095380", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754095380" }, { "id": "rs754095380", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754095380" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KCT->NCT).", "chr_id": "20", "chr_pos": "10672893", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K65", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.670.670", "start_pos": 670, "end_pos": 670, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SYKCICSDGWEGAYCETNIN", "down_seq": "CSQNPCHNGGTCRDLVNDFY", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DCS->NCS).", "chr_id": "20", "chr_pos": "10645461", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D670", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P78504-1.675.675", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P78504-1.680.680", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.675.675", "start_pos": 675, "end_pos": 675, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514513699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514513699", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CSDGWEGAYCETNINDCSQN", "down_seq": "CHNGGTCRDLVNDFYCDCKN", "snv": [ { "evidence": [ { "id": "rs2514513699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514513699" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NLC).", "chr_id": "20", "chr_pos": "10645445", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P675", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P78504-1.670.670", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P78504-1.680.680", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.680.680", "start_pos": 680, "end_pos": 680, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EGAYCETNINDCSQNPCHNG", "down_seq": "TCRDLVNDFYCDCKNGWKGK", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGG->NGS).", "chr_id": "20", "chr_pos": "10645431", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G680", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P78504-1.670.670", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P78504-1.675.675", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P78504-1.700.700", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.700.700", "start_pos": 700, "end_pos": 700, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752584786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752584786", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752584786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752584786", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752584786", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752584786", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GTCRDLVNDFYCDCKNGWKG", "down_seq": "TCHSRDSQCDEATCNNGGTC", "snv": [ { "evidence": [ { "id": "rs752584786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752584786" }, { "id": "rs752584786", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752584786" }, { "id": "rs752584786", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752584786" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KTC->NTC).", "chr_id": "20", "chr_pos": "10645369", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K700", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P78504-1.680.680", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.707.707", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.707.707", "start_pos": 707, "end_pos": 707, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2122603091", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122603091", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2122603091", "url": "https://www.ensembl.org/id/rs2122603091", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NDFYCDCKNGWKGKTCHSRD", "down_seq": "QCDEATCNNGGTCYDEGDAF", "snv": [ { "evidence": [ { "id": "rs2122603091", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122603091" }, { "id": "rs2122603091", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2122603091" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SQC->NQC).", "chr_id": "20", "chr_pos": "10645250", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S707", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P78504-1.700.700", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.744.744", "start_pos": 744, "end_pos": 744, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GDAFKCMCPGGWEGTTCNIA", "down_seq": "NSSCLPNPCHNGGTCVVNGE", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10644977", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R744", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10644976", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R744", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P78504-1.745.745", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P78504-1.746.746", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78504-1.752.752", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.746.746", "start_pos": 746, "end_pos": 746, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2122602515", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122602515", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2122602515", "url": "https://www.ensembl.org/id/rs2122602515", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AFKCMCPGGWEGTTCNIARN", "down_seq": "SCLPNPCHNGGTCVVNGESF", "snv": [ { "evidence": [ { "id": "rs2122602515", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2122602515" }, { "id": "rs2122602515", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2122602515" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSC->NSC).", "chr_id": "20", "chr_pos": "10644970", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S746", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P78504-1.744.744", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P78504-1.745.745", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P78504-1.752.752", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.752.752", "start_pos": 752, "end_pos": 752, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2514512995", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514512995", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PGGWEGTTCNIARNSSCLPN", "down_seq": "CHNGGTCVVNGESFTCVCKE", "snv": [ { "evidence": [ { "id": "rs2514512995", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514512995" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NAC).", "chr_id": "20", "chr_pos": "10644953", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P752", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P78504-1.744.744", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P78504-1.745.745", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P78504-1.746.746", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.794.794", "start_pos": 794, "end_pos": 794, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs865828029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs865828029", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs865828029", "url": "https://www.ensembl.org/id/rs865828029", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WEGPICAQNTNDCSPHPCYN", "down_seq": "GTCVDGDNWYRCECAPGFAG", "snv": [ { "evidence": [ { "id": "rs865828029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs865828029" }, { "id": "rs865828029", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs865828029" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SGT->NGT).", "chr_id": "20", "chr_pos": "10643855", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S794", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P78504-1.795.795", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P78504-1.802.802", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.795.795", "start_pos": 795, "end_pos": 795, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs987799112", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs987799112", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs987799112", "url": "https://www.ncbi.nlm.nih.gov/snp/rs987799112#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs987799112", "url": "http://gnomad.broadinstitute.org/awesome?query=rs987799112", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EGPICAQNTNDCSPHPCYNS", "down_seq": "TCVDGDNWYRCECAPGFAGP", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" }, { "id": "rs987799112", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs987799112" }, { "id": "rs987799112", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs987799112#frequency_tab" }, { "id": "rs987799112", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs987799112" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSG->NSS).", "chr_id": "20", "chr_pos": "10643853", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G795", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P78504-1.794.794", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P78504-1.802.802", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.802.802", "start_pos": 802, "end_pos": 802, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NTNDCSPHPCYNSGTCVDGD", "down_seq": "WYRCECAPGFAGPDCRININ", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "10643831", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N802", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P78504-1.794.794", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P78504-1.795.795", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.878.878", "start_pos": 878, "end_pos": 878, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750102792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750102792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750102792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750102792", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750102792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750102792", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VSGRPCITMGSVIPDGAKWD", "down_seq": "DCNTCQCLNGRIACSKVWCG", "snv": [ { "evidence": [ { "id": "rs750102792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750102792" }, { "id": "rs750102792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750102792" }, { "id": "rs750102792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750102792" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDC->NDC).", "chr_id": "20", "chr_pos": "10641833", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D878", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P78504-1.891.891", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.891.891", "start_pos": 891, "end_pos": 891, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PDGAKWDDDCNTCQCLNGRI", "down_seq": "CSKVWCGPRPCLLHKGHSEC", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "20", "chr_pos": "10641794", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A891", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P78504-1.878.878", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.923.923", "start_pos": 923, "end_pos": 923, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775240101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775240101", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775240101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775240101", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775240101", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775240101#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775240101", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775240101", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLHKGHSECPSGQSCIPILD", "down_seq": "QCFVHPCTGVGECRSSSLQP", "snv": [ { "evidence": [ { "id": "rs775240101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775240101" }, { "id": "rs775240101", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775240101" }, { "id": "rs775240101", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775240101#frequency_tab" }, { "id": "rs775240101", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775240101" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DQC->NQC).", "chr_id": "20", "chr_pos": "10641609", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D923", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.959.959", "start_pos": 959, "end_pos": 959, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1364736945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364736945", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1364736945", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1364736945", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SSLQPVKTKCTSDSYYQDNC", "down_seq": "NITFTFNKEMMSPGLTTEHI", "snv": [ { "evidence": [ { "id": "rs1364736945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364736945" }, { "id": "rs1364736945", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1364736945" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCA->NCT).", "chr_id": "20", "chr_pos": "10641501", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A959", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P78504-1.960.960", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P78504-1.962.962", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.962.962", "start_pos": 962, "end_pos": 962, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs527420845", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420845", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs527420845", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs527420845", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs527420845", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420845", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs527420845", "url": "https://www.ncbi.nlm.nih.gov/snp/rs527420845#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs527420845", "url": "http://gnomad.broadinstitute.org/awesome?query=rs527420845", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs749841384", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749841384", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749841384", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749841384", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749841384", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749841384#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749841384", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749841384", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPVKTKCTSDSYYQDNCANI", "down_seq": "FTFNKEMMSPGLTTEHICSE", "snv": [ { "evidence": [ { "id": "rs527420845", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420845" }, { "id": "rs527420845", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs527420845" }, { "id": "rs527420845", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527420845" }, { "id": "rs527420845", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs527420845#frequency_tab" }, { "id": "rs527420845", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs527420845" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->NIA).", "chr_id": "20", "chr_pos": "10641492", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T962", "disease": [ { "disease_id": "DOID:9245", "recommended_name": { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille syndrome", "description": "A liver disease that is characterized by an accumulation of bile in the liver resulting from a reducted number of liver small bile ducts." }, "synonyms": [ { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Alagille-Watson syndrome", "description": "" }, { "id": "DOID:9245", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9245", "name": "Arteriohepatic dysplasia", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "A genetic condition caused by pathogenic variants in the NOTCH2 gene upstream of those implicated with Hajdu-Cheney syndrome. The mechanism of pathogenicity for Alagille syndrome appears to be haploinsufficiency. Key features include bile duct paucity, cholestasis, congenital heart defects, butterfly vertebrae, posterior embryotoxon, and distinctive facial characteristics. Renal abnormalities may also be present." }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome type 2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome-NOTCH2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille-Watson syndrome due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Arteriohepatic dysplasia due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "syndromic bile duct paucity due to a NOTCH2 point mutation", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "ALGS2", "description": "" }, { "id": "MONDO:0012439", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012439", "name": "Alagille syndrome 2", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "Any Alagille syndrome due to a variation in the JAG1 gene that affects many organ systems including the liver, heart, skeleton, eyes and kidneys." }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome type 1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome-JAG1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille-Watson syndrome due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "arteriohepatic dysplasia due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "syndromic bile duct paucity due to a JAG1 point mutation", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "ALGS1", "description": "" }, { "id": "MONDO:0016862", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016862", "name": "Alagille syndrome 1", "description": "" }, { "id": "MIM:610205", "resource": "MIM", "url": "https://www.omim.org/entry/610205", "name": "Alagille syndrome 2", "description": "Alagille syndrome 2" }, { "id": "MIM:118450", "resource": "MIM", "url": "https://www.omim.org/entry/118450", "name": "Alagille syndrome 1", "description": "Alagille syndrome 1" } ], "unlinked_id_list": [], "evidence": [ { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" }, { "id": "9245", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9245" } ] }, { "disease_id": "DOID:6419", "recommended_name": { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "tetralogy of Fallot", "description": "" }, "synonyms": [ { "id": "DOID:6419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:6419", "name": "Ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy." }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "tetralogy of fallot", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "ventricular septal defect with pulmonary stenosis or atresia, dextraposition of aorta, and hypertrophy of right ventricle", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "Fallot tetralogy", "description": "" }, { "id": "MONDO:0008542", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008542", "name": "TOF", "description": "" }, { "id": "MIM:187500", "resource": "MIM", "url": "https://www.omim.org/entry/187500", "name": "Tetralogy of Fallot", "description": "Tetralogy of Fallot" } ], "unlinked_id_list": [], "evidence": [ { "id": "6419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:6419" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs749841384", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749841384" }, { "id": "rs749841384", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749841384" }, { "id": "rs749841384", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749841384#frequency_tab" }, { "id": "rs749841384", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749841384" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->NIK).", "chr_id": "20", "chr_pos": "10641491", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T962", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P78504-1.959.959", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.960.960", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.987.987", "start_pos": 987, "end_pos": 987, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P78504", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KEMMSPGLTTEHICSELRNL", "down_seq": "ILKNVSAEYSIYIACEPSPS", "snv": [ { "evidence": [ { "id": "P78504", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P78504" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLS).", "chr_id": "20", "chr_pos": "10641201", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N987", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P78504-1.991.991", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P78504-1.993.993", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P78504-1.993.993", "start_pos": 993, "end_pos": 993, "uniprot_canonical_ac": "P78504-1", "length": 1218, "uniprot_id": "JAG1_HUMAN", "protein_name": "Protein jagged-1", "refseq_ac": "NP_000205", "refseq_name": "protein jagged-1 precursor", "gene_name": "JAG1", "gene_names_uniprotkb": "JAG1; JAGL1", "gene_names_refseq": "AGS1; AGS; AHD; AWS; CD339; CMT2HH; DCHE; HJ1; JAG1; JAGL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P78504", "url": "https://www.uniprot.org/uniprotkb/P78504" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1351971291", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351971291", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1351971291", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1351971291#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2514508409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514508409", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLTTEHICSELRNLNILKNV", "down_seq": "AEYSIYIACEPSPSANNEIH", "snv": [ { "evidence": [ { "id": "rs1351971291", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1351971291" }, { "id": "rs1351971291", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1351971291#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVA).", "chr_id": "20", "chr_pos": "10641184", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S993", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2514508409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2514508409" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVF).", "chr_id": "20", "chr_pos": "10641183", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S993", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1064", "end_pos": "1064" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "86", "end_pos": "110" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "991", "end_pos": "991" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "207", "end_pos": "207" } ] }, { "type": "snv", "site_list": [ { "start_pos": "217", "end_pos": "217" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1103", "end_pos": "1103" }, { "start_pos": "1109", "end_pos": "1109" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1160", "end_pos": "1160" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "471", "end_pos": "471" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "527", "end_pos": "527" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "707", "end_pos": "707" }, { "start_pos": "744", "end_pos": "744" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "746", "end_pos": "746" }, { "start_pos": "752", "end_pos": "752" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "878", "end_pos": "878" }, { "start_pos": "891", "end_pos": "891" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "959", "end_pos": "959" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "987", "end_pos": "987" }, { "start_pos": "991", "end_pos": "991" }, { "start_pos": "993", "end_pos": "993" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P78504-1.987.987", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P78504-1.991.991", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs764436953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764436953", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764436953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764436953", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764436953", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764436953#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764436953", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764436953", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs759164196", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759164196", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759164196", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759164196", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVLVVVGGQALEEEEAGEEP", "down_seq": "PGLGNFAFYNSKAKRWMALP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr289", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs764436953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764436953" }, { "id": "rs764436953", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764436953" }, { "id": "rs764436953", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764436953#frequency_tab" }, { "id": "rs764436953", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764436953" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "2", "chr_pos": "238142890", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T289", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759164196", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759164196" }, { "id": "rs759164196", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759164196" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "2", "chr_pos": "238142889", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T289", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q0D2K2-1.296.296", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.413.413", "start_pos": 413, "end_pos": 413, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Studying the O-GlcNAcome of human placentas using banked tissue samples.", "journal": "Glycobiology", "date": "2024-01-22", "authors": "Luna Sarai, Malard Florian, Pereckas Michaela, Aoki Mayumi, Aoki Kazahiro, Olivier-Van Stichelen Stephanie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q0D2K2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q0D2K2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "rs1236177694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236177694", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1236177694", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236177694#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESYDPYTDSWTPVSPALKYV", "down_seq": "NFSAAGCRGRLYLVGSSACK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser413", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q0D2K2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2" } ] } ], "snv": [ { "evidence": [ { "id": "rs1236177694", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1236177694" }, { "id": "rs1236177694", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1236177694#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->R).", "chr_id": "2", "chr_pos": "238147922", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S413", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q0D2K2-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q0D2K2-1.416.416", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q0D2K2-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Studying the O-GlcNAcome of human placentas using banked tissue samples.", "journal": "Glycobiology", "date": "2024-01-22", "authors": "Luna Sarai, Malard Florian, Pereckas Michaela, Aoki Mayumi, Aoki Kazahiro, Olivier-Van Stichelen Stephanie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q0D2K2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q0D2K2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "rs747297027", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747297027", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747297027", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747297027", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747297027", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747297027#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747297027", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747297027", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DPYTDSWTPVSPALKYVSNF", "down_seq": "AAGCRGRLYLVGSSACKYNA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser416", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q0D2K2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q0D2K2" } ] } ], "snv": [ { "evidence": [ { "id": "rs747297027", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747297027" }, { "id": "rs747297027", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747297027" }, { "id": "rs747297027", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747297027#frequency_tab" }, { "id": "rs747297027", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747297027" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "2", "chr_pos": "238147930", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S416", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q0D2K2-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q0D2K2-1.413.413", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q0D2K2-1.575.575", "start_pos": 575, "end_pos": 575, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1483560642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483560642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1483560642", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483560642", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760655844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760655844", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760655844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760655844", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760655844", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760655844#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760655844", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760655844", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YHGASTVFLDVSKWTQPSGP", "down_seq": "QEH", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr575", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1483560642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483560642" }, { "id": "rs1483560642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483560642" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "2", "chr_pos": "238151051", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T575", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760655844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760655844" }, { "id": "rs760655844", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760655844" }, { "id": "rs760655844", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760655844#frequency_tab" }, { "id": "rs760655844", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760655844" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "2", "chr_pos": "238151052", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T575", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1483560642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483560642" }, { "id": "rs1483560642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1483560642" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "2", "chr_pos": "238151051", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T575", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q0D2K2-1.573.573", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778622350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778622350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778622350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778622350", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778622350", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778622350#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778622350", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778622350", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GQALEEEEAGEEPTPGLGNF", "down_seq": "FYNSKAKRWMALPDFPDYHK", "snv": [ { "evidence": [ { "id": "rs778622350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778622350" }, { "id": "rs778622350", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778622350" }, { "id": "rs778622350", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778622350#frequency_tab" }, { "id": "rs778622350", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778622350" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFA->NFT).", "chr_id": "2", "chr_pos": "238142910", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A296", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q0D2K2-1.289.289", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777774313", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777774313", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777774313", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777774313", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777774313", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777774313#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777774313", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777774313", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ALPDFPDYHKWGFSLAALNN", "down_seq": "IYVTGGSRGTKTDTWSTTQA", "snv": [ { "evidence": [ { "id": "rs777774313", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777774313" }, { "id": "rs777774313", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777774313" }, { "id": "rs777774313", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777774313#frequency_tab" }, { "id": "rs777774313", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777774313" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNN->NNS).", "chr_id": "2", "chr_pos": "238144974", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N327", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q0D2K2-1.329.329", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q0D2K2-1.341.341", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs557191254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557191254", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs557191254", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557191254", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs557191254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557191254", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs557191254", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557191254", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PDFPDYHKWGFSLAALNNNI", "down_seq": "VTGGSRGTKTDTWSTTQAWC", "snv": [ { "evidence": [ { "id": "rs557191254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557191254" }, { "id": "rs557191254", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557191254" }, { "id": "rs557191254", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557191254" }, { "id": "rs557191254", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557191254" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIY->NIC).", "chr_id": "2", "chr_pos": "238144980", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y329", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q0D2K2-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q0D2K2-1.341.341", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1216361597", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216361597", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1216361597", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216361597#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1216361597", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216361597", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LAALNNNIYVTGGSRGTKTD", "down_seq": "WSTTQAWCFPLKEASWKPVA", "snv": [ { "evidence": [ { "id": "rs1216361597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216361597" }, { "id": "rs1216361597", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1216361597#frequency_tab" }, { "id": "rs1216361597", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216361597" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TWS->NWS).", "chr_id": "2", "chr_pos": "238145704", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T341", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q0D2K2-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q0D2K2-1.329.329", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1200369408", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200369408", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1200369408", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1200369408#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1200369408", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200369408", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SHAQDMLDGLQRLRSQPKLA", "down_seq": "VTLLVGGRELPCHRGLLALS", "snv": [ { "evidence": [ { "id": "rs1200369408", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200369408" }, { "id": "rs1200369408", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1200369408#frequency_tab" }, { "id": "rs1200369408", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200369408" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "2", "chr_pos": "238140854", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D34", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1402295617", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402295617", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1402295617", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402295617", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "FPLKEASWKPVAPMLKPRTN", "down_seq": "ASAALNGEIYVIGGTTLDVV", "snv": [ { "evidence": [ { "id": "rs1402295617", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402295617" }, { "id": "rs1402295617", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402295617" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HAS->NAS).", "chr_id": "2", "chr_pos": "238145790", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H370", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q0D2K2-1.371.371", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369675751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369675751", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369675751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369675751", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369675751", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369675751#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369675751", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369675751", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PLKEASWKPVAPMLKPRTNH", "down_seq": "SAALNGEIYVIGGTTLDVVE", "snv": [ { "evidence": [ { "id": "rs369675751", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369675751" }, { "id": "rs369675751", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369675751" }, { "id": "rs369675751", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369675751#frequency_tab" }, { "id": "rs369675751", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369675751" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHA->NHT).", "chr_id": "2", "chr_pos": "238145793", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A371", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q0D2K2-1.370.370", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.401.401", "start_pos": 401, "end_pos": 401, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs887450499", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887450499", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs887450499", "url": "https://www.ncbi.nlm.nih.gov/snp/rs887450499#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VIGGTTLDVVEVESYDPYTD", "down_seq": "WTPVSPALKYVSNFSAAGCR", "snv": [ { "evidence": [ { "id": "rs887450499", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887450499" }, { "id": "rs887450499", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs887450499#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SWT->NWT).", "chr_id": "2", "chr_pos": "238147885", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S401", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q0D2K2-1.413.413", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q0D2K2-1.416.416", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1382190274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382190274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1382190274", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382190274", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "LYLIGDNTKKVYVYDPGANL", "down_seq": "QKVQSQHSLHENGALVPLGD", "snv": [ { "evidence": [ { "id": "rs1382190274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382190274" }, { "id": "rs1382190274", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382190274" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLW->NLC).", "chr_id": "2", "chr_pos": "238149146", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W493", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q0D2K2-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q0D2K2-1.507.507", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q0D2K2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YDPGANLWQKVQSQHSLHEN", "down_seq": "ALVPLGDALYVTGGRWQGME", "snv": [ { "evidence": [ { "id": "Q0D2K2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "238150844", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G506", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q0D2K2-1.493.493", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q0D2K2-1.507.507", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.507.507", "start_pos": 507, "end_pos": 507, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773445797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773445797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773445797", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773445797#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773445797", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773445797", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q0D2K2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DPGANLWQKVQSQHSLHENG", "down_seq": "LVPLGDALYVTGGRWQGMEG", "snv": [ { "evidence": [ { "id": "rs773445797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797" }, { "id": "rs773445797", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797" }, { "id": "rs773445797", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773445797#frequency_tab" }, { "id": "rs773445797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773445797" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "2", "chr_pos": "238150847", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A507", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q0D2K2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2" }, { "id": "rs773445797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797" }, { "id": "rs773445797", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773445797" }, { "id": "rs773445797", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773445797#frequency_tab" }, { "id": "rs773445797", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773445797" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "2", "chr_pos": "238150847", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A507", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q0D2K2-1.493.493", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q0D2K2-1.506.506", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1692744088", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1692744088", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1692744088", "url": "https://www.ensembl.org/id/rs1692744088", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YVTGGRWQGMEGDYHVEMEA", "down_seq": "DTVRDTWTRHGALPRLWLYH", "snv": [ { "evidence": [ { "id": "rs1692744088", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1692744088" }, { "id": "rs1692744088", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1692744088" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YDT->NDT).", "chr_id": "2", "chr_pos": "238150934", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y536", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q0D2K2-1.542.542", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.542.542", "start_pos": 542, "end_pos": 542, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q0D2K2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WQGMEGDYHVEMEAYDTVRD", "down_seq": "WTRHGALPRLWLYHGASTVF", "snv": [ { "evidence": [ { "id": "Q0D2K2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TWT->NWT).", "chr_id": "2", "chr_pos": "238150953", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T542", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q0D2K2-1.536.536", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.573.573", "start_pos": 573, "end_pos": 573, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q0D2K2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WLYHGASTVFLDVSKWTQPS", "down_seq": "PTQEH", "snv": [ { "evidence": [ { "id": "Q0D2K2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "238151045", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G573", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q0D2K2-1.575.575", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q0D2K2-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "Q0D2K2-1", "length": 578, "uniprot_id": "KLH30_HUMAN", "protein_name": "Kelch-like protein 30", "refseq_ac": "NP_940984", "refseq_name": "kelch-like protein 30", "gene_name": "KLHL30", "gene_names_uniprotkb": "KLHL30", "gene_names_refseq": "KLHL30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q0D2K2", "url": "https://www.uniprot.org/uniprotkb/Q0D2K2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q0D2K2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FAGDFAESFSARVELRDVEP", "down_seq": "VVGQLVDFVYTGRLTITQGN", "snv": [ { "evidence": [ { "id": "Q0D2K2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q0D2K2" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "238140998", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A82", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "289", "end_pos": "289" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "542", "end_pos": "542" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.475.475", "start_pos": 475, "end_pos": 475, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1349452126", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349452126", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1349452126", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349452126#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1349452126", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349452126", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKLPNWQMEVSKLNDIALPP", "down_seq": "PAPTQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr475", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1349452126", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1349452126" }, { "id": "rs1349452126", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1349452126#frequency_tab" }, { "id": "rs1349452126", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1349452126" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "8", "chr_pos": "102650151", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T475", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" }, { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q13118", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LCNHQTCPMKAASILNYQNN", "down_seq": "FRRRTHLNVEAARKNIPCAA", "snv": [ { "evidence": [ { "id": "Q13118", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "102651781", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S184", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "site_lbl": "Ser184" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q13118-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13118-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1438256445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438256445", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1438256445", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438256445#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1438256445", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438256445", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "CNHQTCPMKAASILNYQNNS", "down_seq": "RRRTHLNVEAARKNIPCAAV", "snv": [ { "evidence": [ { "id": "rs1438256445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438256445" }, { "id": "rs1438256445", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1438256445#frequency_tab" }, { "id": "rs1438256445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438256445" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSF->NSS).", "chr_id": "8", "chr_pos": "102651778", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F185", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q13118-1.184.184", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13118-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1347602560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347602560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1347602560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1347602560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1347602560", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347602560", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QNNSFRRRTHLNVEAARKNI", "down_seq": "CAAVSPNRSKCERNTVADVD", "snv": [ { "evidence": [ { "id": "rs1347602560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347602560" }, { "id": "rs1347602560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1347602560#frequency_tab" }, { "id": "rs1347602560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347602560" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "8", "chr_pos": "102651731", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P201", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13118-1.184.184", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q13118-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13118-1.206.206", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1314460095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314460095", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1314460095", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314460095", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SKCERNTVADVDEKASAALY", "down_seq": "FSVPSSETVICRSQPAPVSP", "snv": [ { "evidence": [ { "id": "rs1314460095", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314460095" }, { "id": "rs1314460095", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314460095" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DFS->NFS).", "chr_id": "8", "chr_pos": "102651644", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D230", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q13118-1.249.249", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1827176198", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1827176198", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1827176198", "url": "https://www.ensembl.org/id/rs1827176198", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YFKSSHLKAHTRTHTGEKPF", "down_seq": "CSWKGCERRFARSDELSRHR", "snv": [ { "evidence": [ { "id": "rs1827176198", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1827176198" }, { "id": "rs1827176198", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1827176198" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SCS->NCS).", "chr_id": "8", "chr_pos": "102650376", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q13118-1.384.384", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13118", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FACPMCDRRFMRSDHLTKHA", "down_seq": "RHLSAKKLPNWQMEVSKLND", "snv": [ { "evidence": [ { "id": "Q13118", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "102650230", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R449", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13118-1.445.445", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13118-1.450.450", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.450.450", "start_pos": 450, "end_pos": 450, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13118", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ACPMCDRRFMRSDHLTKHAR", "down_seq": "HLSAKKLPNWQMEVSKLNDI", "snv": [ { "evidence": [ { "id": "Q13118", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13118" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "102650227", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R450", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13118-1.445.445", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13118-1.449.449", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1353479917", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353479917", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1353479917", "url": "https://www.ensembl.org/id/rs1353479917", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SWNKTAEKSDFEAVEALMSM", "down_seq": "CSWKSDFKKYVENRPVTPVS", "snv": [ { "evidence": [ { "id": "rs1353479917", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353479917" }, { "id": "rs1353479917", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1353479917" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SCS->NCS).", "chr_id": "8", "chr_pos": "102652288", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q13118-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13118-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1827233525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1827233525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1827233525", "url": "https://www.ensembl.org/id/rs1827233525", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ALMSMSCSWKSDFKKYVENR", "down_seq": "VTPVSDLSEEENLLPGTPDF", "snv": [ { "evidence": [ { "id": "rs1827233525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1827233525" }, { "id": "rs1827233525", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1827233525" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRP->NRS).", "chr_id": "8", "chr_pos": "102652244", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P64", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q13118-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13118-1.66.66", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13118-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CDK2 phosphorylation regulates the protein stability of KLF10 by interfering with binding of the E3 ligase SIAH1.", "journal": "Biochimica et biophysica acta", "date": "2015", "authors": "Lin CH, Lin SY, Chang HW, Ko LJ, Tseng YS, Chang VH, Yu WC", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "25728284", "url": "https://glygen.org/publication/PubMed/25728284" } ] } ], "crossref": [ { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25728284", "url": "https://glygen.org/publication/PubMed/25728284", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRRTHLNVEAARKNIPCAAV", "down_seq": "PNRSKCERNTVADVDEKASA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P24941-1", "kinase_gene_name": "CDK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "25728284", "url": "https://glygen.org/publication/PubMed/25728284" } ], "site_lbl": "Ser206" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13118-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" }, { "database": "iPTMnet", "id": "Q13118-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q13118-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] } ], "crossref": [ { "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YDFSVPSSETVICRSQPAPV", "down_seq": "PQQKSVLVSPPAVSAGGVPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ], "site_lbl": "Ser249" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13118-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Transforming growth factor-beta-inducible early response gene 1 is a novel substrate for atypical protein kinase Cs.", "journal": "Cellular and molecular life sciences : CMLS", "date": "2011", "authors": "Alemu EA, Sjottem E, Outzen H, Larsen KB, Holm T, Bjorkoy G, Johansen T", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893" } ] } ], "crossref": [ { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRIRSHICSHPGCGKTYFKS", "down_seq": "HLKAHTRTHTGEKPFSCSWK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893" } ], "site_lbl": "Ser384" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q13118-1.400.400", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Transforming growth factor-beta-inducible early response gene 1 is a novel substrate for atypical protein kinase Cs.", "journal": "Cellular and molecular life sciences : CMLS", "date": "2011", "authors": "Alemu EA, Sjottem E, Outzen H, Larsen KB, Holm T, Bjorkoy G, Johansen T", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893" } ] } ], "crossref": [ { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GEKKFACPMCDRRFMRSDHL", "down_seq": "KHARRHLSAKKLPNWQMEVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "20953893", "url": "https://glygen.org/publication/PubMed/20953893" } ], "site_lbl": "Thr445" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q13118-1.449.449", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13118-1.450.450", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.", "journal": "Nature communications", "date": "2016-11-21", "authors": "Bassani-Sternberg Michal, Br\u00e4unlein Eva, Klar Richard, Engleitner Thomas, Sinitcyn Pavel, Audehm Stefan, Straub Melanie, Weber Julia, Slotta-Huspenina Julia, Specht Katja, Martignoni Marc E, Werner Angelika, Hein R\u00fcdiger, H Busch Dirk, Peschel Christian, Rad Roland, Cox J\u00fcrgen, Mann Matthias, Krackhardt Angela M", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ] } ], "crossref": [ { "id": "Q13118", "url": "https://www.iedb.org/epitope/Q13118", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSMSCSWKSDFKKYVENRPV", "down_seq": "PVSDLSEEENLLPGTPDFHT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q13118", "url": "https://www.iedb.org/epitope/Q13118" }, { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ], "site_lbl": "Thr66" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13118-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13118-1.64.64", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13118-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "Q13118-1", "length": 480, "uniprot_id": "KLF10_HUMAN", "protein_name": "Krueppel-like factor 10", "refseq_ac": "NP_001027453", "refseq_name": "Krueppel-like factor 10 isoform b", "gene_name": "KLF10", "gene_names_uniprotkb": "KLF10; TIEG1; TIEG", "gene_names_refseq": "EGR-alpha; EGRA; KLF10; TIEG1; TIEG", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13118", "url": "https://www.uniprot.org/uniprotkb/Q13118" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Destabilization of KLF10, a tumor suppressor, relies on thr93 phosphorylation and isomerase association.", "journal": "Biochimica et biophysica acta", "date": "2013", "authors": "Hwang YC, Yang CH, Lin CH, Ch'ang HJ, Chang VHS, Yu WCY", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" } ], "reference": [ { "type": "PubMed", "id": "23994618", "url": "https://glygen.org/publication/PubMed/23994618" } ] } ], "crossref": [ { "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23994618", "url": "https://glygen.org/publication/PubMed/23994618", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EEENLLPGTPDFHTIPAFCL", "down_seq": "PPYSPSDFEPSQVSNLMAPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13118", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13118" }, { "database": "PubMed", "id": "23994618", "url": "https://glygen.org/publication/PubMed/23994618" } ], "site_lbl": "Thr93" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "475", "end_pos": "475" } ] }, { "type": "snv", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "450", "end_pos": "450" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "64", "end_pos": "64" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "184", "end_pos": "184" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "93", "end_pos": "93" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14500-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ASPLFGISRQDLETDDFEIV", "down_seq": "ILEGMVEATAMTTQARSSYL", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "29", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); patient count (29/2670).", "chr_id": "17", "chr_pos": "21416231", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V297", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14500-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14500-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14500-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.314.314", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SWLLFGIIFWVIAVAHGDLE", "down_seq": "AEGRGRTPCVMQVHGFMAAF", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415683", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P114", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q14500-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IIFWVIAVAHGDLEPAEGRG", "down_seq": "TPCVMQVHGFMAAFLFSIET", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415700", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R120", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14500-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.140.140", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MTAASRANPYSI", "down_seq": "SSEEDGLHLVTMSGANGFGN", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415379", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V13", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q14500-1.30.30", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RTPCVMQVHGFMAAFLFSIE", "down_seq": "QTTIGYGLRCVTEECPVAVF", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415761", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T140", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14500-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14500-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14500-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14500-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PCVMQVHGFMAAFLFSIETQ", "down_seq": "TIGYGLRCVTEECPVAVFMV", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415767", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T142", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14500-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GFMAAFLFSIETQTTIGYGL", "down_seq": "CVTEECPVAVFMVVAQSIVG", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "17", "chr_pos": "21415788", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R149", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q14500-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14500-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14500-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14500-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AAFLFSIETQTTIGYGLRCV", "down_seq": "EECPVAVFMVVAQSIVGCII", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415797", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T152", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14500-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14500-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14500-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ETQTTIGYGLRCVTEECPVA", "down_seq": "FMVVAQSIVGCIIDSFMIGA", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415817", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V159", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14500-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14500-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14500-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14500-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14500-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GYGLRCVTEECPVAVFMVVA", "down_seq": "SIVGCIIDSFMIGAIMAKMA", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "21415835", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q165", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14500-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14500-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14500-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.185.185", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QSIVGCIIDSFMIGAIMAKM", "down_seq": "RPKKRAQTLLFSHNAVVALR", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415895", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A185", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14500-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14500-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14500-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SIVGCIIDSFMIGAIMAKMA", "down_seq": "PKKRAQTLLFSHNAVVALRD", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "21415900", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R186", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q14500-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DSFMIGAIMAKMARPKKRAQ", "down_seq": "LLFSHNAVVALRDGKLCLMW", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415920", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T193", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14500-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14500-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14500-1.201.201", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MAKMARPKKRAQTLLFSHNA", "down_seq": "VALRDGKLCLMWRVGNLRKS", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415943", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V201", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14500-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14500-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14500-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.214.214", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLFSHNAVVALRDGKLCLMW", "down_seq": "VGNLRKSHIVEAHVRAQLIK", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "17", "chr_pos": "21415983", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R214", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14500-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.229.229", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LCLMWRVGNLRKSHIVEAHV", "down_seq": "AQLIKPRVTEEGEYIPLDQI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416028", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R229", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14500-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14500-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VGNLRKSHIVEAHVRAQLIK", "down_seq": "RVTEEGEYIPLDQIDIDVGF", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416046", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P235", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14500-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14500-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14500-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GNLRKSHIVEAHVRAQLIKP", "down_seq": "VTEEGEYIPLDQIDIDVGFD", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416048", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R236", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q14500-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14500-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14500-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RKSHIVEAHVRAQLIKPRVT", "down_seq": "EGEYIPLDQIDIDVGFDKGL", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "17", "chr_pos": "21416057", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E239", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14500-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14500-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14500-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.245.245", "start_pos": 245, "end_pos": 245, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EAHVRAQLIKPRVTEEGEYI", "down_seq": "LDQIDIDVGFDKGLDRIFLV", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "17", "chr_pos": "21416076", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P245", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14500-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14500-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14500-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14500-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14500-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.262.262", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AQLIKPRVTEEGEYIPLDQI", "down_seq": "IDVGFDKGLDRIFLVSPITI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416090", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D250", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14500-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14500-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14500-1.239.239", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14500-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14500-1.262.262", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GEYIPLDQIDIDVGFDKGLD", "down_seq": "IFLVSPITILHEIDEASPLF", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416124", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R261", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14500-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14500-1.272.272", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EYIPLDQIDIDVGFDKGLDR", "down_seq": "FLVSPITILHEIDEASPLFG", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416127", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I262", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14500-1.245.245", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q14500-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14500-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DVGFDKGLDRIFLVSPITIL", "down_seq": "EIDEASPLFGISRQDLETDD", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "H", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "21416157", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H272", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q14500-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14500-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14500-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.289.289", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "IFLVSPITILHEIDEASPLF", "down_seq": "ISRQDLETDDFEIVVILEGM", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416186", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G282", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14500-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TILHEIDEASPLFGISRQDL", "down_seq": "TDDFEIVVILEGMVEATAMT", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416207", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E289", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14500-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14500-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14500-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YSIVSSEEDGLHLVTMSGAN", "down_seq": "FGNGKVHTRRRCRNRFVKKN", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415430", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G30", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14500-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14500-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FEIVVILEGMVEATAMTTQA", "down_seq": "SSYLANEILWGHRFEPVLFE", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416280", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R313", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14500-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14500-1.314.314", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIVVILEGMVEATAMTTQAR", "down_seq": "SYLANEILWGHRFEPVLFEE", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "21416284", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S314", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14500-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14500-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.334.334", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SSYLANEILWGHRFEPVLFE", "down_seq": "KNQYKIDYSHFHKTYEVPST", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416342", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E334", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14500-1.343.343", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.354.354", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.343.343", "start_pos": 343, "end_pos": 343, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WGHRFEPVLFEEKNQYKIDY", "down_seq": "HFHKTYEVPSTPRCSAKDLV", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "589", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416370", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S343", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q14500-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14500-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.354.354", "start_pos": 354, "end_pos": 354, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EKNQYKIDYSHFHKTYEVPS", "down_seq": "PRCSAKDLVENKFLLPSANS", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416403", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T354", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14500-1.343.343", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14500-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NQYKIDYSHFHKTYEVPSTP", "down_seq": "CSAKDLVENKFLLPSANSFC", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416409", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R356", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14500-1.343.343", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14500-1.354.354", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SAKDLVENKFLLPSANSFCY", "down_seq": "NELAFLSRDEEDEADGDQDG", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21416474", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E378", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q14500-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14500-1.392.392", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LLPSANSFCYENELAFLSRD", "down_seq": "EDEADGDQDGRSRDGLSPQA", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416504", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E388", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14500-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14500-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.405.405", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DGLHLVTMSGANGFGNGKVH", "down_seq": "RRRCRNRFVKKNGQCNIEFA", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415455", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T38", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14500-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14500-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14500-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14500-1.58.58", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ANSFCYENELAFLSRDEEDE", "down_seq": "DGDQDGRSRDGLSPQARHDF", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21416517", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A392", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14500-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14500-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.405.405", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RSRDGLSPQARHDFDRLQAG", "down_seq": "GVLEQRPYRRESEI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "21416598", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G419", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q14500-1.405.405", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14500-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q14500-1.431.431", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "HDFDRLQAGGGVLEQRPYRR", "down_seq": "SEI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "2", "frequency": "2.2", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: patient freq. (2.2%).", "chr_id": "17", "chr_pos": "21416631", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E430", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q14500-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14500-1.431.431", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VTMSGANGFGNGKVHTRRRC", "down_seq": "NRFVKKNGQCNIEFANMDEK", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415470", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R43", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14500-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14500-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14500-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14500-1.62.62", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MSGANGFGNGKVHTRRRCRN", "down_seq": "FVKKNGQCNIEFANMDEKSQ", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415475", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R45", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415476", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R45", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14500-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14500-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14500-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14500-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14500-1.62.62", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TRRRCRNRFVKKNGQCNIEF", "down_seq": "NMDEKSQRYLADMFTTCVDI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415514", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A58", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14500-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14500-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14500-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14500-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14500-1.66.66", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "CRNRFVKKNGQCNIEFANMD", "down_seq": "KSQRYLADMFTTCVDIRWRY", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415526", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E62", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14500-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14500-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14500-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14500-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14500-1.81.81", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FVKKNGQCNIEFANMDEKSQ", "down_seq": "YLADMFTTCVDIRWRYMLLI", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "21415538", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R66", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14500-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14500-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14500-1.81.81", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14500", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DEKSQRYLADMFTTCVDIRW", "down_seq": "YMLLIFSLAFLASWLLFGII", "snv": [ { "evidence": [ { "id": "Q14500", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14500" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "21415583", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R81", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14500-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14500-1.66.66", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14500-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRDEEDEADGDQDGRSRDGL", "down_seq": "PQARHDFDRLQAGGGVLEQR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser405" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14500-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14500-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14500-1.419.419", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14500-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q14500-1", "length": 433, "uniprot_id": "KCJ12_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 12", "refseq_ac": "NP_066292", "refseq_name": "ATP-sensitive inward rectifier potassium channel 12", "gene_name": "KCNJ12", "gene_names_uniprotkb": "KCNJ12; IRK2; KCNJN1", "gene_names_refseq": "IRK-2; IRK2; KCNJ12; KCNJN1; Kir2.2; hIRK1; hIRK; hkir2.2x; kcnj12x", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14500", "url": "https://www.uniprot.org/uniprotkb/Q14500" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Inward rectifier potassium channel Kir2.2 is associated with synapse-associated protein SAP97.", "journal": "Journal of cell science", "date": "2001", "authors": "Leonoudakis D, Mailliard W, Wingerd K, Clegg D, Vandenberg C", "evidence": [ { "database": "iPTMnet", "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500" } ], "reference": [ { "type": "PubMed", "id": "11181181", "url": "https://glygen.org/publication/PubMed/11181181" } ] } ], "crossref": [ { "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11181181", "url": "https://glygen.org/publication/PubMed/11181181", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DFDRLQAGGGVLEQRPYRRE", "down_seq": "EI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P17612-1", "kinase_gene_name": "PRKACA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500" }, { "database": "PubMed", "id": "11181181", "url": "https://glygen.org/publication/PubMed/11181181" } ], "site_lbl": "Ser431" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14500", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14500" }, { "database": "PubMed", "id": "11181181", "url": "https://glygen.org/publication/PubMed/11181181" } ], "site_lbl": "Ser431" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "297", "end_pos": "297" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "405", "end_pos": "405" }, { "start_pos": "431", "end_pos": "431" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q14500-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14500-1.430.430", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q15726-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q15726-1", "length": 138, "uniprot_id": "KISS1_HUMAN", "protein_name": "Metastasis-suppressor KiSS-1", "refseq_ac": "NP_002247", "refseq_name": "metastasis-suppressor KiSS-1 preproprotein", "gene_name": "KISS1", "gene_names_uniprotkb": "KISS1; PP5098", "gene_names_refseq": "HH13; KISS1; KiSS-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15726", "url": "https://www.uniprot.org/uniprotkb/Q15726" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry.", "journal": "Analytical chemistry", "date": "2004", "authors": "Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC", "evidence": [ { "database": "UniProtKB", "id": "Q15726", "url": "https://www.uniprot.org/uniprotkb/Q15726" }, { "database": "iPTMnet", "id": "Q15726", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15726" } ], "reference": [ { "type": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" } ] } ], "crossref": [ { "id": "Q15726", "url": "https://www.uniprot.org/uniprotkb/Q15726", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q15726", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15726", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RQIPAPQGAVLVQREKDLPN", "down_seq": "NWNSFGLRFGKREAAPGNHG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q15726", "url": "https://www.uniprot.org/uniprotkb/Q15726" }, { "database": "PubMed", "id": "15144186", "url": "https://glygen.org/publication/PubMed/15144186" }, { "database": "iPTMnet", "id": "Q15726", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15726" } ], "site_lbl": "Tyr112" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3LI61-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "Q3LI61-1", "length": 65, "uniprot_id": "KR202_HUMAN", "protein_name": "Keratin-associated protein 20-2", "refseq_ac": "NP_853647", "refseq_name": "keratin-associated protein 20-2", "gene_name": "KRTAP20-2", "gene_names_uniprotkb": "KRTAP20-2; KAP20.2", "gene_names_refseq": "KAP20.2; KRTAP20-2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI61", "url": "https://www.uniprot.org/uniprotkb/Q3LI61" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI61", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI61", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MCYYSNYYGGL", "down_seq": "YGYGVLGGGYGCGCGYGHGY", "snv": [ { "evidence": [ { "id": "Q3LI61", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI61" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30635297", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R12", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q3LI61", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI61" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "21", "chr_pos": "30635298", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R12", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "20", "end_pos": "20" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q3LI61-1.20.20", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI61-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "Q3LI61-1", "length": 65, "uniprot_id": "KR202_HUMAN", "protein_name": "Keratin-associated protein 20-2", "refseq_ac": "NP_853647", "refseq_name": "keratin-associated protein 20-2", "gene_name": "KRTAP20-2", "gene_names_uniprotkb": "KRTAP20-2; KAP20.2", "gene_names_refseq": "KAP20.2; KRTAP20-2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI61", "url": "https://www.uniprot.org/uniprotkb/Q3LI61" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI61", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI61", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "", "down_seq": "GYGCGCGYGHGYGGLGCGYG", "snv": [ { "evidence": [ { "id": "Q3LI61", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI61" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30635321", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G20", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "20", "end_pos": "20" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q3LI61-1.12.12", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q3LI81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81" }, { "database": "O-GlcNAc Atlas", "id": "Q3LI81", "url": "https://oglcnac.org/atlas/detail/Q3LI81" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] } ], "crossref": [ { "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q3LI81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q3LI81", "url": "https://oglcnac.org/atlas/detail/Q3LI81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AQSCQPASLKGNSCPPKTSK", "down_seq": "KNFETLERASSQCQCQSQNP", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser148", "evidence": [ { "id": "31637018", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31637018" }, { "id": "Q3LI81", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81" }, { "id": "Q3LI81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q3LI81" } ] } ], "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "21", "chr_pos": "30337226", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S148", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "21", "chr_pos": "30337226", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S148", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q3LI81-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q3LI81-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3LI81-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q3LI81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81" }, { "database": "O-GlcNAc Atlas", "id": "Q3LI81", "url": "https://oglcnac.org/atlas/detail/Q3LI81" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] } ], "crossref": [ { "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q3LI81", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q3LI81", "url": "https://oglcnac.org/atlas/detail/Q3LI81", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1282164345", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282164345", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1282164345", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282164345", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PASLKGNSCPPKTSKSKNFE", "down_seq": "LERASSQCQCQSQNPESSSC", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr153", "evidence": [ { "id": "31637018", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31637018" }, { "id": "Q3LI81", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q3LI81" }, { "id": "Q3LI81", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q3LI81" } ] } ], "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" }, { "id": "rs1282164345", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282164345" }, { "id": "rs1282164345", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282164345" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "21", "chr_pos": "30337211", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T153", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q3LI81-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q3LI81-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q3LI81-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q3LI81-1.171.171", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q3LI81-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SQPCQSESTQQMGFVAQSCQ", "down_seq": "ASLKGNSCPPKTSKSKNFET", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30337271", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P133", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q3LI81-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q3LI81-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MGFVAQSCQPASLKGNSCPP", "down_seq": "TSKSKNFETLERASSQCQCQ", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KTS->NTS).", "chr_id": "21", "chr_pos": "30337237", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K144", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q3LI81-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q3LI81-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QPASLKGNSCPPKTSKSKNF", "down_seq": "TLERASSQCQCQSQNPESSS", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30337215", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E152", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q3LI81-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q3LI81-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q3LI81-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q3LI81-1.171.171", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761066424", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761066424", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761066424", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761066424", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761066424", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761066424#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761066424", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761066424", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSCPPKTSKSKNFETLERAS", "down_seq": "QCQCQSQNPESSSCRPLVNV", "snv": [ { "evidence": [ { "id": "rs761066424", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761066424" }, { "id": "rs761066424", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761066424" }, { "id": "rs761066424", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761066424#frequency_tab" }, { "id": "rs761066424", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761066424" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SQC->NQC).", "chr_id": "21", "chr_pos": "30337193", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S159", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q3LI81-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q3LI81-1.148.148", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q3LI81-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q3LI81-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1443161321", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443161321", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443161321", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443161321#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1443161321", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443161321", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MPHSHCHSLRSFHNA", "down_seq": "PLSAITHGTNPITFEDRLCL", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" }, { "id": "rs1443161321", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443161321" }, { "id": "rs1443161321", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443161321#frequency_tab" }, { "id": "rs1443161321", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443161321" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAP->NAS).", "chr_id": "21", "chr_pos": "30337623", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P16", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAP->NAT).", "chr_id": "21", "chr_pos": "30337623", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P16", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q3LI81-1.4.4", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1364730737", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364730737", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1364730737", "url": "https://www.ensembl.org/id/rs1364730737", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FETLERASSQCQCQSQNPES", "down_seq": "SCRPLVNVAPEPQLLESSPG", "snv": [ { "evidence": [ { "id": "rs1364730737", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1364730737" }, { "id": "rs1364730737", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1364730737" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSC->NSC).", "chr_id": "21", "chr_pos": "30337157", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q3LI81-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q3LI81-1.153.153", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q3LI81-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SQCQCQSQNPESSSCRPLVN", "down_seq": "APEPQLLESSPGVEPTCCVT", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30337134", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V179", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q3LI81-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q3LI81-1.171.171", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373116371", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373116371", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373116371", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373116371", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373116371", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373116371#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373116371", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373116371", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MPH", "down_seq": "HCHSLRSFHNAPPLSAITHG", "snv": [ { "evidence": [ { "id": "rs373116371", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373116371" }, { "id": "rs373116371", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373116371" }, { "id": "rs373116371", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373116371#frequency_tab" }, { "id": "rs373116371", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373116371" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SHC->NHC).", "chr_id": "21", "chr_pos": "30337658", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S4", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q3LI81-1.16.16", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ETCNETTSCQMTNCEQDLFT", "down_seq": "DSCVQSNCFPGVVQTTYSNS", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "21", "chr_pos": "30337455", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D72", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q3LI81-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q3LI81-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q3LI81-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs927078704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927078704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs927078704", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927078704#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs927078704", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927078704", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TCNETTSCQMTNCEQDLFTD", "down_seq": "SCVQSNCFPGVVQTTYSNSR", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" }, { "id": "rs927078704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927078704" }, { "id": "rs927078704", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927078704#frequency_tab" }, { "id": "rs927078704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927078704" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSC->NSC).", "chr_id": "21", "chr_pos": "30337452", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D73", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q3LI81-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q3LI81-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q3LI81-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q3LI81", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSCQMTNCEQDLFTDDSCVQ", "down_seq": "NCFPGVVQTTYSNSRPCERT", "snv": [ { "evidence": [ { "id": "Q3LI81", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q3LI81" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SNC->NNC).", "chr_id": "21", "chr_pos": "30337436", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S78", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q3LI81-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q3LI81-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q3LI81-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q3LI81-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "Q3LI81-1", "length": 207, "uniprot_id": "KR271_HUMAN", "protein_name": "Keratin-associated protein 27-1", "refseq_ac": "NP_001071179", "refseq_name": "keratin-associated protein 27-1", "gene_name": "KRTAP27-1", "gene_names_uniprotkb": "KRTAP27-1; KAP27.1", "gene_names_refseq": "KRTAP27-1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q3LI81", "url": "https://www.uniprot.org/uniprotkb/Q3LI81" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757425315", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757425315", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757425315", "url": "https://www.ensembl.org/id/rs757425315", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DLFTDDSCVQSNCFPGVVQT", "down_seq": "YSNSRPCERTACQSESSSAG", "snv": [ { "evidence": [ { "id": "rs757425315", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757425315" }, { "id": "rs757425315", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs757425315" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TYS->NYS).", "chr_id": "21", "chr_pos": "30337406", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T88", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "148", "end_pos": "148" }, { "start_pos": "153", "end_pos": "153" } ] }, { "type": "snv", "site_list": [ { "start_pos": "133", "end_pos": "133" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "88", "end_pos": "88" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q3LI81-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q3LI81-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q3LI81-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1711.1711", "start_pos": 1711, "end_pos": 1711, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" }, { "database": "O-GlcNAc Atlas", "id": "Q5TCS8", "url": "https://oglcnac.org/atlas/detail/Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5TCS8", "url": "https://oglcnac.org/atlas/detail/Q5TCS8", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YVPPLAPHPLPSADMIPKRL", "down_seq": "LSELKSRFPKCAELQGYCPV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1711", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q5TCS8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q5TCS8", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q5TCS8" } ] } ], "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "6", "chr_pos": "109497881", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T1711", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q5TCS8-4.1718.1718", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q5TCS8-4.1723.1723", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5TCS8-4.541.541", "start_pos": 541, "end_pos": 541, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" }, { "database": "O-GlcNAc Atlas", "id": "Q5TCS8", "url": "https://oglcnac.org/atlas/detail/Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5TCS8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5TCS8", "url": "https://oglcnac.org/atlas/detail/Q5TCS8", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs936330932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936330932", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs936330932", "url": "https://www.ensembl.org/id/rs936330932", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1456534232", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456534232", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1456534232", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456534232#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1456534232", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456534232", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KSENVLHDQAAKVDKDDGKE", "down_seq": "GETFTFKRHSQDASQDVKLY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr541", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q5TCS8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5TCS8" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q5TCS8", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q5TCS8" } ] } ], "snv": [ { "evidence": [ { "id": "rs936330932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs936330932" }, { "id": "rs936330932", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs936330932" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "6", "chr_pos": "109612082", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T541", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1456534232", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1456534232" }, { "id": "rs1456534232", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1456534232#frequency_tab" }, { "id": "rs1456534232", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1456534232" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "6", "chr_pos": "109612081", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T541", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5TCS8-4.1072.1072", "start_pos": 1072, "end_pos": 1072, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AKQELEELAIQANVKVEEEN", "down_seq": "KKQLPEVQLTEEEEVIKSSL", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109545877", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1072", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1117.1117", "start_pos": 1117, "end_pos": 1117, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PLPPEILEVILSEWWLKEPI", "down_seq": "STGFILDGFPRYPEEAQFLG", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109542048", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1117", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1139.1139", "start_pos": 1139, "end_pos": 1139, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TGFILDGFPRYPEEAQFLGD", "down_seq": "GFFPDAAVFIQVDDQDIFDR", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109533406", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1139", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q5TCS8-4.1159.1159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1159.1159", "start_pos": 1159, "end_pos": 1159, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RGFFPDAAVFIQVDDQDIFD", "down_seq": "LLPAQIEKWKLKQKKKLERK", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109533345", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1159", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q5TCS8-4.1139.1139", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1192.1192", "start_pos": 1192, "end_pos": 1192, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QKKKLERKKLIKDMKAKIRV", "down_seq": "TIAKRRAELILERDKKRREN", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "6", "chr_pos": "109529070", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D1192", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1298.1298", "start_pos": 1298, "end_pos": 1298, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1234578134", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234578134", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1234578134", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1234578134#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1234578134", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234578134", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LQIIQDELERYLIPIISING", "down_seq": "RRNHIVQYTLNMKLKPLVEN", "snv": [ { "evidence": [ { "id": "rs1234578134", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1234578134" }, { "id": "rs1234578134", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1234578134#frequency_tab" }, { "id": "rs1234578134", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1234578134" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "6", "chr_pos": "109516030", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1298", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q5TCS8-4.1303.1303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1303.1303", "start_pos": 1303, "end_pos": 1303, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1208659668", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208659668", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1208659668", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208659668#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1208659668", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208659668", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "DELERYLIPIISINGARRNH", "down_seq": "VQYTLNMKLKPLVENRASIF", "snv": [ { "evidence": [ { "id": "rs1208659668", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208659668" }, { "id": "rs1208659668", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208659668#frequency_tab" }, { "id": "rs1208659668", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208659668" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHI->NHS).", "chr_id": "6", "chr_pos": "109516014", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1303", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1208659668", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208659668" }, { "id": "rs1208659668", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208659668#frequency_tab" }, { "id": "rs1208659668", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208659668" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHI->NHT).", "chr_id": "6", "chr_pos": "109516014", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1303", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q5TCS8-4.1298.1298", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q5TCS8-4.1319.1319", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q5TCS8-4.1320.1320", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1319.1319", "start_pos": 1319, "end_pos": 1319, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RRNHIVQYTLNMKLKPLVEN", "down_seq": "ASIFEKCHPIPAPLAQKMLT", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109515967", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1319", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q5TCS8-4.1303.1303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q5TCS8-4.1320.1320", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1320.1320", "start_pos": 1320, "end_pos": 1320, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760646402", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760646402", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760646402", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760646402", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760646402", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760646402", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RNHIVQYTLNMKLKPLVENR", "down_seq": "SIFEKCHPIPAPLAQKMLTF", "snv": [ { "evidence": [ { "id": "rs760646402", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760646402" }, { "id": "rs760646402", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760646402" }, { "id": "rs760646402", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760646402" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRT).", "chr_id": "6", "chr_pos": "109515964", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1320", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q5TCS8-4.1303.1303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q5TCS8-4.1319.1319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1355.1355", "start_pos": 1355, "end_pos": 1355, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QKMLTFTYKYISSFGYWDPV", "down_seq": "LSEGETIKPVENAENPIYPV", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "6", "chr_pos": "109515857", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1355", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1488.1488", "start_pos": 1488, "end_pos": 1488, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1347567440", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347567440", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1347567440", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1347567440#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1347567440", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347567440", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KGMTAPDELAIQALELSLME", "down_seq": "VCNTAGVVIDGYPVTKHQMN", "snv": [ { "evidence": [ { "id": "rs1347567440", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347567440" }, { "id": "rs1347567440", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1347567440#frequency_tab" }, { "id": "rs1347567440", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347567440" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SVC->NVC).", "chr_id": "6", "chr_pos": "109509197", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1488", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1510.1510", "start_pos": 1510, "end_pos": 1510, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1289160682", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289160682", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1289160682", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1289160682#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "CNTAGVVIDGYPVTKHQMNL", "down_seq": "EARSIIPMVIFELSVPSKEI", "snv": [ { "evidence": [ { "id": "rs1289160682", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289160682" }, { "id": "rs1289160682", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1289160682#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLL->NLS).", "chr_id": "6", "chr_pos": "109506753", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1510", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1800129674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1800129674", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1800129674", "url": "https://www.ensembl.org/id/rs1800129674", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LIKNLNLKPDVIINIKCPDY", "down_seq": "LCQRISGQRQHNNTGYIYSR", "snv": [ { "evidence": [ { "id": "rs1800129674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1800129674" }, { "id": "rs1800129674", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1800129674" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLC->NLC).", "chr_id": "6", "chr_pos": "109659401", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D153", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q5TCS8-4.167.167", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1552.1552", "start_pos": 1552, "end_pos": 1552, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KRLLLEKENEQRLPYPLHNS", "down_seq": "QIVAVNNVKYRKNIGEIRQY", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "6", "chr_pos": "109506522", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1552", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1655.1655", "start_pos": 1655, "end_pos": 1655, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs958762420", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs958762420", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs958762420", "url": "https://www.ensembl.org/id/rs958762420", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RLGEFEQFCPVSLAESQELF", "down_seq": "CSATDSLEFAAEFRGHYYKM", "snv": [ { "evidence": [ { "id": "rs958762420", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs958762420" }, { "id": "rs958762420", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs958762420" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DCS->NCS).", "chr_id": "6", "chr_pos": "109499127", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1655", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IKCPDYDLCQRISGQRQHNN", "down_seq": "GYIYSRDQWDPEVIENHRKK", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109659358", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T167", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q5TCS8-4.153.153", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1684.1684", "start_pos": 1684, "end_pos": 1684, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1777241474", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1777241474", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1777241474", "url": "https://www.ensembl.org/id/rs1777241474", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FAAEFRGHYYKMSSQEKLNK", "down_seq": "LENPELYVPPLAPHPLPSAD", "snv": [ { "evidence": [ { "id": "rs1777241474", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1777241474" }, { "id": "rs1777241474", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1777241474" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKF->NKS).", "chr_id": "6", "chr_pos": "109497961", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F1684", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1718.1718", "start_pos": 1718, "end_pos": 1718, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HPLPSADMIPKRLTLSELKS", "down_seq": "FPKCAELQGYCPVTYKDGNQ", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109497860", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1718", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q5TCS8-4.1711.1711", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q5TCS8-4.1723.1723", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1723.1723", "start_pos": 1723, "end_pos": 1723, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ADMIPKRLTLSELKSRFPKC", "down_seq": "ELQGYCPVTYKDGNQRYEAL", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109497844", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1723", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q5TCS8-4.1711.1711", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q5TCS8-4.1718.1718", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1757.1757", "start_pos": 1757, "end_pos": 1757, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NQRYEALVPGSINYALEYHN", "down_seq": "IYICENKEKLQKFLRSPLKY", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109497511", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1757", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q5TCS8-4.1773.1773", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1773.1773", "start_pos": 1773, "end_pos": 1773, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EYHNRIYICENKEKLQKFLR", "down_seq": "PLKYWEQKLPHKLPPLREPI", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109495438", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1773", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q5TCS8-4.1757.1757", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1819.1819", "start_pos": 1819, "end_pos": 1819, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PLPGYLEQGIATSLIKAMNA", "down_seq": "GCLKPKFPFLSIRRSALLYI", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "6", "chr_pos": "109494058", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1819", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753780601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753780601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753780601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753780601", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753780601", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753780601", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KTEEYPFADIFDEDETERNF", "down_seq": "LSKPVCFVVFGKPGVGKTTL", "snv": [ { "evidence": [ { "id": "rs753780601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753780601" }, { "id": "rs753780601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753780601" }, { "id": "rs753780601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753780601" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFL->NFS).", "chr_id": "6", "chr_pos": "109675669", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L26", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747876029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747876029", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747876029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747876029", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747876029", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747876029#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747876029", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747876029", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QTLEEVMAEHNPQYLIELNG", "down_seq": "KPAEELFMIVMDRLKYLNLK", "snv": [ { "evidence": [ { "id": "rs747876029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747876029" }, { "id": "rs747876029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747876029" }, { "id": "rs747876029", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747876029#frequency_tab" }, { "id": "rs747876029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747876029" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGN->NGS).", "chr_id": "6", "chr_pos": "109644639", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q5TCS8-4.272.272", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1465152725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465152725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1465152725", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1465152725#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1465152725", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465152725", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LEEVMAEHNPQYLIELNGNK", "down_seq": "AEELFMIVMDRLKYLNLKRA", "snv": [ { "evidence": [ { "id": "rs1465152725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465152725" }, { "id": "rs1465152725", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1465152725#frequency_tab" }, { "id": "rs1465152725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465152725" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKS).", "chr_id": "6", "chr_pos": "109644634", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P272", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q5TCS8-4.270.270", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.354.354", "start_pos": 354, "end_pos": 354, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KWGRTCPVNLKDGNIYSGLP", "down_seq": "YSVSFLGKIYCLSSEEALKP", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DYS->NYS).", "chr_id": "6", "chr_pos": "109633197", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D354", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1029694771", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1029694771", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1029694771", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1029694771#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1029694771", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1029694771", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "YAQLVQPRFDKARETLVENT", "down_seq": "AEATAAAIKVVKEKLLRELQ", "snv": [ { "evidence": [ { "id": "rs1029694771", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1029694771" }, { "id": "rs1029694771", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1029694771#frequency_tab" }, { "id": "rs1029694771", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1029694771" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTI->NTT).", "chr_id": "6", "chr_pos": "109619166", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I442", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.635.635", "start_pos": 635, "end_pos": 635, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1789463227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1789463227", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1789463227", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1789463227", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VMEENKDRFPGAPKYGGWIV", "down_seq": "NCPIVKELWMALIKKGIIPD", "snv": [ { "evidence": [ { "id": "rs1789463227", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1789463227" }, { "id": "rs1789463227", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1789463227" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNC->NNC).", "chr_id": "6", "chr_pos": "109586012", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D635", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q5TCS8-4.638.638", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.638.638", "start_pos": 638, "end_pos": 638, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1789461845", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1789461845", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1789461845", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1789461845#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ENKDRFPGAPKYGGWIVDNC", "down_seq": "IVKELWMALIKKGIIPDLVI", "snv": [ { "evidence": [ { "id": "rs1789461845", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1789461845" }, { "id": "rs1789461845", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1789461845#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCP->NCS).", "chr_id": "6", "chr_pos": "109586003", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P638", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q5TCS8-4.635.635", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.678.678", "start_pos": 678, "end_pos": 678, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IYLSDTENNGKCLFNRIYLQ", "down_seq": "KSEIDSKILERLLEELQKKK", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKS->NKS).", "chr_id": "6", "chr_pos": "109585203", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K678", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q5TCS8-4.682.682", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.682.682", "start_pos": 682, "end_pos": 682, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "DTENNGKCLFNRIYLQKKSE", "down_seq": "DSKILERLLEELQKKKKEEE", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (IDS->NDS).", "chr_id": "6", "chr_pos": "109585192", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I682", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q5TCS8-4.678.678", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.720.720", "start_pos": 720, "end_pos": 720, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775154259", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775154259", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775154259", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775154259", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775154259", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775154259#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775154259", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775154259", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EEEEARKATEEELRLEEENR", "down_seq": "LLELMKVKAKEAEETDNEDE", "snv": [ { "evidence": [ { "id": "rs775154259", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775154259" }, { "id": "rs775154259", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775154259" }, { "id": "rs775154259", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775154259#frequency_tab" }, { "id": "rs775154259", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775154259" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRS).", "chr_id": "6", "chr_pos": "109579581", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R720", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.797.797", "start_pos": 797, "end_pos": 797, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309892071", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309892071", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309892071", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309892071#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1309892071", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309892071", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TEPEAVSEPIEETTVETEIP", "down_seq": "GSKEGLEIEKLSETVVLPEF", "snv": [ { "evidence": [ { "id": "rs1309892071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309892071" }, { "id": "rs1309892071", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309892071#frequency_tab" }, { "id": "rs1309892071", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309892071" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KGS->NGS).", "chr_id": "6", "chr_pos": "109564799", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K797", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q5TCS8-4.807.807", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.807.807", "start_pos": 807, "end_pos": 807, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1464991231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464991231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1464991231", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464991231", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EETTVETEIPKGSKEGLEIE", "down_seq": "LSETVVLPEFPEDSYPDVPE", "snv": [ { "evidence": [ { "id": "rs1464991231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464991231" }, { "id": "rs1464991231", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464991231" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "6", "chr_pos": "109564769", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K807", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q5TCS8-4.797.797", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.863.863", "start_pos": 863, "end_pos": 863, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1786161922", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1786161922", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1786161922", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1786161922#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1786161922", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1786161922", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KQLEATISEAYIKILNLEIA", "down_seq": "RTPQELLQKVVETMEKPFQY", "snv": [ { "evidence": [ { "id": "rs1786161922", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1786161922" }, { "id": "rs1786161922", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1786161922#frequency_tab" }, { "id": "rs1786161922", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1786161922" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRT->NRT).", "chr_id": "6", "chr_pos": "109564128", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D863", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.925.925", "start_pos": 925, "end_pos": 925, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5TCS8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVDEELEEEEEEEGEDKMKE", "down_seq": "KRHLGDTKHFCPVVLKENFI", "snv": [ { "evidence": [ { "id": "Q5TCS8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5TCS8" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "109550280", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R925", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q5TCS8-4.945.945", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.945.945", "start_pos": 945, "end_pos": 945, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775761909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775761909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775761909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775761909", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775761909", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775761909#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775761909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775761909", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RKRHLGDTKHFCPVVLKENF", "down_seq": "LQPGNTEEAAKYREKIYYFS", "snv": [ { "evidence": [ { "id": "rs775761909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775761909" }, { "id": "rs775761909", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775761909" }, { "id": "rs775761909", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775761909#frequency_tab" }, { "id": "rs775761909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775761909" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFI->NFT).", "chr_id": "6", "chr_pos": "109550220", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I945", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q5TCS8-4.925.925", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5TCS8-4.1034.1034", "start_pos": 1034, "end_pos": 1034, "uniprot_canonical_ac": "Q5TCS8-4", "length": 1911, "uniprot_id": "KAD9_HUMAN", "protein_name": "Adenylate kinase 9", "refseq_ac": "NP_001138600", "refseq_name": "adenylate kinase 9 isoform 1", "gene_name": "AK9", "gene_names_uniprotkb": "AK9; AKD1; AKD2; C6orf199; C6orf224", "gene_names_refseq": "AK 9; AK9; AKD1; AKD2; C6orf199; C6orf224; SPGF89; dJ70A9.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5TCS8", "url": "https://www.uniprot.org/uniprotkb/Q5TCS8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deciphering the landscape of phosphorylated HLA-II ligands.", "journal": "iScience", "date": "2022-05-20", "authors": "Solleder Marthe, Racle Julien, Guillaume Philippe, Coukos George, Bassani-Sternberg Michal, Gfeller David", "evidence": [ { "database": "iPTMnet", "id": "Q5TCS8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5TCS8" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q5TCS8", "url": "https://www.iedb.org/epitope/Q5TCS8", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q5TCS8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5TCS8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KLNIFHIQFEEVLQEKLLLK", "down_seq": "EKKVGPEFEEDSENEQAAKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q5TCS8", "url": "https://www.iedb.org/epitope/Q5TCS8" }, { "database": "iPTMnet", "id": "Q5TCS8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5TCS8" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr1034" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "541", "end_pos": "541" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1117", "end_pos": "1117" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1192", "end_pos": "1192" }, { "start_pos": "1298", "end_pos": "1298" }, { "start_pos": "1303", "end_pos": "1303" }, { "start_pos": "1319", "end_pos": "1319" }, { "start_pos": "1320", "end_pos": "1320" }, { "start_pos": "1355", "end_pos": "1355" }, { "start_pos": "1488", "end_pos": "1488" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "1552", "end_pos": "1552" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "1684", "end_pos": "1684" }, { "start_pos": "1711", "end_pos": "1711" }, { "start_pos": "1718", "end_pos": "1718" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1757", "end_pos": "1757" }, { "start_pos": "1773", "end_pos": "1773" }, { "start_pos": "1819", "end_pos": "1819" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "635", "end_pos": "635" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "682", "end_pos": "682" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "797", "end_pos": "797" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "863", "end_pos": "863" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "945", "end_pos": "945" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1034", "end_pos": "1034" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68DU8-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification.", "journal": "Talanta", "date": "2017", "authors": "Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q68DU8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DU8" } ], "reference": [ { "type": "PubMed", "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811" } ] } ], "crossref": [ { "id": "28411811", "url": "https://glygen.org/publication/PubMed/28411811", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68DU8", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DU8", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "28411811", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28411811" }, { "id": "Q68DU8", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68DU8" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68DU8-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DAKFRRVPRILVCGRISLAK", "down_seq": "VFGETLNESRDPDRAPERYT", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144207321", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E203", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q68DU8-1.217.217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RISLAKEVFGETLNESRDPD", "down_seq": "APERYTSRFYLKFKHLERAF", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144207364", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R217", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q68DU8-1.203.203", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AFDMLSECGFHMVACNSSVT", "down_seq": "SFINQYTDDKIWSSYTEYVF", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144207480", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A256", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SSYTEYVFYREPSRWSPSHC", "down_seq": "CCCKNGKGDKEGESGTSCND", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144473692", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D289", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TSSCDSQSEASSPQETVICG", "down_seq": "VTRQTNIQTLDRPIKKGPVQ", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "P", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "144473821", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "P332", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q68DU8-1.344.344", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PQETVICGPVTRQTNIQTLD", "down_seq": "PIKKGPVQLIQQSEMRRKSD", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144473857", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R344", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68DU8-1.332.332", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KKGPVQLIQQSEMRRKSDLL", "down_seq": "TLTSGSRESNMSSKKKAVKE", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144473926", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R367", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SNMSSKKKAVKEKLSIEEEL", "down_seq": "KCIQDFLKIKIPDRFPERKH", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144474015", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E396", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q68DU8-1.402.402", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "KKAVKEKLSIEEELEKCIQD", "down_seq": "LKIKIPDRFPERKHPWQSEL", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "F", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "144474032", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F402", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q68DU8-1.396.396", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FTRHSTLISIPHSLLWKMFS", "down_seq": "KRDTANDLAKDSKGRFFIDR", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "144206883", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P57", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RDTANDLAKDSKGRFFIDRD", "down_seq": "FLFRYILDYLRDRQVVLPDH", "snv": [ { "evidence": [ { "id": "Q68DU8", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68DU8" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "5", "chr_pos": "144206950", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G79", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q68DU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DU8" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q68DU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DU8", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RQVVLPDHFPEKGRLKREAE", "down_seq": "FQLPDLVKLLTPDEIKQSPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" }, { "database": "iPTMnet", "id": "Q68DU8", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68DU8" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr112" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q68DU8-1.130.130", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68DU8-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEYFQLPDLVKLLTPDEIKQ", "down_seq": "PDEFCHSDFEDASQGSDTRI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "site_lbl": "Ser130" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68DU8-1.112.112", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q68DU8-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q68DU8-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68DU8-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLVKLLTPDEIKQSPDEFCH", "down_seq": "DFEDASQGSDTRICPPSSLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "site_lbl": "Ser137" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q68DU8-1.130.130", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68DU8-1.143.143", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68DU8-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPDEIKQSPDEFCHSDFEDA", "down_seq": "QGSDTRICPPSSLLPADRKW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "site_lbl": "Ser143" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q68DU8-1.130.130", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68DU8-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q68DU8-1.146.146", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68DU8-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "Q68DU8-1", "length": 428, "uniprot_id": "KCD16_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD16", "refseq_ac": "NP_065819", "refseq_name": "BTB/POZ domain-containing protein KCTD16", "gene_name": "KCTD16", "gene_names_uniprotkb": "KCTD16; KIAA1317", "gene_names_refseq": "KCTD16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIKQSPDEFCHSDFEDASQG", "down_seq": "DTRICPPSSLLPADRKWGFI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68DU8", "url": "https://www.uniprot.org/uniprotkb/Q68DU8" } ], "site_lbl": "Ser146" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "203", "end_pos": "203" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "146", "end_pos": "146" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68DU8-1.130.130", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68DU8-1.137.137", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q68DU8-1.143.143", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" }, { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSASNNSPPLTNITPTQKLP", "down_seq": "PVNQATLSQTQGSEKLLVSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr251", "evidence": [ { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "Q86T24", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q86T24", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" } ], "site_lbl": "Thr251" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q86T24-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q86T24-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q86T24-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86T24-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q86T24-1.257.257", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T24-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "title": "Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.", "journal": "Molecular & cellular proteomics : MCP", "date": "2021", "authors": "Maynard JC, Chalkley RJ", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2057620449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057620449", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057620449", "url": "https://www.ensembl.org/id/rs2057620449", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPPLTNITPTQKLPTPVNQA", "down_seq": "LSQTQGSEKLLVSSAPTHLT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr257", "evidence": [ { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "Q86T24", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q86T24", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86T24" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "snv": [ { "evidence": [ { "id": "rs2057620449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057620449" }, { "id": "rs2057620449", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057620449" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "X", "chr_pos": "120254184", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T257", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q86T24-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q86T24-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q86T24-1.251.251", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q86T24-1.256.256", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T24-1.502.502", "start_pos": 502, "end_pos": 502, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "database": "O-GlcNAc Atlas", "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86T24", "url": "https://oglcnac.org/atlas/detail/Q86T24", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DHYELIVDGRVYYICIVCKR", "down_seq": "YVCLTSLRRHFNIHSWEKKY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser502", "evidence": [ { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "Q86T24", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86T24" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q86T24", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86T24" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T24-1.552.552", "start_pos": 552, "end_pos": 552, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Kaiso is a genome-wide repressor of transcription that is essential for amphibian development.", "journal": "Development (Cambridge, England)", "date": "2004", "authors": "Ruzov A, Dunican DS, Prokhortchouk A, Pennings S, Stancheva I, Prokhortchouk E, Meehan RR", "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "15548582", "url": "https://glygen.org/publication/PubMed/15548582" } ] } ], "crossref": [ { "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15548582", "url": "https://glygen.org/publication/PubMed/15548582", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "PLAEYRTKHEIHHTGERRYQ", "down_seq": "LACGKSFINYQFMSSHIKSV", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "R", "comment": "Abrogates both sequence-specific and methylation-dependent DNA-binding.", "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" }, { "database": "PubMed", "id": "15548582", "url": "https://glygen.org/publication/PubMed/15548582" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q86T24-1.543.543", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T24-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AQDNGATIMPIITESFSLSA", "down_seq": "DYEMKKIIVTDSDDDDDDVI", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "120253941", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E176", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q86T24-1.194.194", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SAEDYEMKKIIVTDSDDDDD", "down_seq": "VIFCSEILPTKETLPSNNTV", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "23", "chr_pos": "120253995", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D194", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q86T24-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1556014847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556014847", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1556014847", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556014847", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTVAQVQSNPGPVAISDVAP", "down_seq": "ASNNSPPLTNITPTQKLPTP", "snv": [ { "evidence": [ { "id": "rs1556014847", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556014847" }, { "id": "rs1556014847", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556014847" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAS->NAS).", "chr_id": "X", "chr_pos": "120254110", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q86T24-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q86T24-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86T24-1.251.251", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs782738766", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782738766", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs782738766", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782738766", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs782738766", "url": "https://www.ncbi.nlm.nih.gov/snp/rs782738766#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs782738766", "url": "http://gnomad.broadinstitute.org/awesome?query=rs782738766", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QSNPGPVAISDVAPSASNNS", "down_seq": "PLTNITPTQKLPTPVNQATL", "snv": [ { "evidence": [ { "id": "rs782738766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782738766" }, { "id": "rs782738766", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782738766" }, { "id": "rs782738766", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs782738766#frequency_tab" }, { "id": "rs782738766", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs782738766" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "X", "chr_pos": "120254127", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P238", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q86T24-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q86T24-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q86T24-1.251.251", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86T24-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86T24-1.257.257", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142932677", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142932677", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142932677", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142932677", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs142932677", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142932677", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142932677", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142932677#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142932677", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142932677", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NSPPLTNITPTQKLPTPVNQ", "down_seq": "TLSQTQGSEKLLVSSAPTHL", "snv": [ { "evidence": [ { "id": "rs142932677", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142932677" }, { "id": "rs142932677", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs142932677" }, { "id": "rs142932677", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142932677" }, { "id": "rs142932677", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142932677#frequency_tab" }, { "id": "rs142932677", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142932677" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQA->NQS).", "chr_id": "X", "chr_pos": "120254181", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A256", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q86T24-1.237.237", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q86T24-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86T24-1.251.251", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q86T24-1.257.257", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs782714211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782714211", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs782714211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782714211", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs782714211", "url": "http://gnomad.broadinstitute.org/awesome?query=rs782714211", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DTISSSPDSAVSNTSLVPQA", "down_seq": "TSQNTSFDGSLIQKMQIPTL", "snv": [ { "evidence": [ { "id": "rs782714211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782714211" }, { "id": "rs782714211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs782714211" }, { "id": "rs782714211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs782714211" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTS->NTS).", "chr_id": "X", "chr_pos": "120254493", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D360", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1360578532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360578532", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360578532", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360578532#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1360578532", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360578532", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LLQEPLSNSLKISDIITRNT", "down_seq": "DPGVGSKHLMEGQKIITLDT", "snv": [ { "evidence": [ { "id": "rs1360578532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360578532" }, { "id": "rs1360578532", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1360578532#frequency_tab" }, { "id": "rs1360578532", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360578532" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "X", "chr_pos": "120254614", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q86T24-1.402.402", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1556015019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556015019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1556015019", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556015019", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QEPLSNSLKISDIITRNTND", "down_seq": "GVGSKHLMEGQKIITLDTAT", "snv": [ { "evidence": [ { "id": "rs1556015019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556015019" }, { "id": "rs1556015019", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556015019" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDP->NDT).", "chr_id": "X", "chr_pos": "120254619", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P402", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q86T24-1.400.400", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SLNEQRGHGLFCDVTVIVED", "down_seq": "KFRAHKNILSASSTYFHQLF", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "120253537", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R41", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.428.428", "start_pos": 428, "end_pos": 428, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLMEGQKIITLDTATEIEGL", "down_seq": "TGCKVYANIGEDTYDIVIPV", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "120254698", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S428", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q86T24-1.438.438", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q86T24-1.442.442", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.438.438", "start_pos": 438, "end_pos": 438, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LDTATEIEGLSTGCKVYANI", "down_seq": "EDTYDIVIPVKDDPDEGEAR", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIG->NIS).", "chr_id": "23", "chr_pos": "120254727", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G438", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q86T24-1.428.428", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q86T24-1.442.442", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.543.543", "start_pos": 543, "end_pos": 543, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1556015145", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556015145", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1556015145", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556015145", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "PCRYCEKVFPLAEYRTKHEI", "down_seq": "HTGERRYQCLACGKSFINYQ", "snv": [ { "evidence": [ { "id": "rs1556015145", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556015145" }, { "id": "rs1556015145", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1556015145" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HHT->NHT).", "chr_id": "X", "chr_pos": "120255042", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H543", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q86T24-1.552.552", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.602.602", "start_pos": 602, "end_pos": 602, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T24", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs781875913", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781875913", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781875913", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781875913", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs781875913", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781875913", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781875913", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781875913", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KLYRLHPCRSLQIRQYAYLS", "down_seq": "RSSTIPAMKDDGIGYKVDTG", "snv": [ { "evidence": [ { "id": "Q86T24", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T24" }, { "id": "rs781875913", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781875913" }, { "id": "rs781875913", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781875913" }, { "id": "rs781875913", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781875913" }, { "id": "rs781875913", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781875913" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DRS->NRS).", "chr_id": "23", "chr_pos": "120255219", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D602", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs912573988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912573988", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs912573988", "url": "https://www.ncbi.nlm.nih.gov/snp/rs912573988#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs912573988", "url": "http://gnomad.broadinstitute.org/awesome?query=rs912573988", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YKVDTGKEPPVGTTTSTQNK", "down_seq": "MTWEDIFIQQENDSIFKQNV", "snv": [ { "evidence": [ { "id": "rs912573988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912573988" }, { "id": "rs912573988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs912573988#frequency_tab" }, { "id": "rs912573988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs912573988" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKS).", "chr_id": "X", "chr_pos": "120255324", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P637", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs912573988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs912573988" }, { "id": "rs912573988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs912573988#frequency_tab" }, { "id": "rs912573988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs912573988" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKT).", "chr_id": "X", "chr_pos": "120255324", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P637", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T24-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQSNPGPVAISDVAPSASNN", "down_seq": "PPLTNITPTQKLPTPVNQAT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser237" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q86T24-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q86T24-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q86T24-1.251.251", "categories": [ "glycosylation_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86T24-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q86T24-1.257.257", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T24-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q86T24-1", "length": 672, "uniprot_id": "KAISO_HUMAN", "protein_name": "Transcriptional regulator Kaiso", "refseq_ac": "NP_001171671", "refseq_name": "transcriptional regulator Kaiso", "gene_name": "ZBTB33", "gene_names_uniprotkb": "ZBTB33; KAISO; ZNF348", "gene_names_refseq": "ZBTB33; ZNF-kaiso; ZNF348", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T24", "url": "https://www.uniprot.org/uniprotkb/Q86T24" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.", "journal": "Nature biotechnology", "date": "2005", "authors": "Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" } ], "reference": [ { "type": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" } ] } ], "crossref": [ { "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TEIEGLSTGCKVYANIGEDT", "down_seq": "DIVIPVKDDPDEGEARLENE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86T24", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T24" }, { "database": "PubMed", "id": "15592455", "url": "https://glygen.org/publication/PubMed/15592455" } ], "site_lbl": "Tyr442" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "502", "end_pos": "502" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "552", "end_pos": "552" } ] }, { "type": "snv", "site_list": [ { "start_pos": "176", "end_pos": "176" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "543", "end_pos": "543" }, { "start_pos": "602", "end_pos": "602" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "237", "end_pos": "237" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "442", "end_pos": "442" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q86T24-1.428.428", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q86T24-1.438.438", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IXL9-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AALIAYATRERAVIKLQSLV", "down_seq": "MWRVRWRYCQVLNAIYIIQG", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51863206", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R111", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8IXL9-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IXL9-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IAYATRERAVIKLQSLVRMW", "down_seq": "VRWRYCQVLNAIYIIQGHWQ", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "3", "chr_pos": "51863215", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R114", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8IXL9-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IXL9-1.118.118", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TRERAVIKLQSLVRMWRVRW", "down_seq": "YCQVLNAIYIIQGHWQCHNC", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "51863227", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R118", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8IXL9-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IXL9-1.114.114", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLNAIYIIQGHWQCHNCQTC", "down_seq": "LLQGHCVVTATHLQFHIEII", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51863299", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A142", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MRV", "down_seq": "FCTKGNLILVIIEDVEESIE", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51861676", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R4", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRIRTKAAVKIQAWWRGTLV", "down_seq": "RTLLHAALRAWIIQCWWRMT", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51863053", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R60", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q8IXL9-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVRRTLLHAALRAWIIQCWW", "down_seq": "MTLSRVLEKKRQAALIAYAT", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51863107", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R78", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IXL9-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IXL9-1.82.82", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXL9-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "Q8IXL9-1", "length": 164, "uniprot_id": "IQCF2_HUMAN", "protein_name": "IQ domain-containing protein F2", "refseq_ac": "NP_982248", "refseq_name": "IQ domain-containing protein F2", "gene_name": "IQCF2", "gene_names_uniprotkb": "IQCF2", "gene_names_refseq": "IQCF2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXL9", "url": "https://www.uniprot.org/uniprotkb/Q8IXL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLLHAALRAWIIQCWWRMTL", "down_seq": "RVLEKKRQAALIAYATRERA", "snv": [ { "evidence": [ { "id": "Q8IXL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXL9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51863120", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S82", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IXL9-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MTNNSGSKAEL", "down_seq": "VGGKYKLVRKIGSGSFGDVY", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37105223", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V12", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8N752-1.24.24", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HLIGTVRYASINAHLGIEQS", "down_seq": "RDDMESLGYVFMYFNRTSLP", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37104659", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R200", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NSGSKAELVVGGKYKLVRKI", "down_seq": "SGSFGDVYLGITTTNGEDVA", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37105187", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G24", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8N752-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8N752-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8N752-1.42.42", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GFPAEFAMYLNYCRGLRFEE", "down_seq": "PDYMYLRQLFRILFRTLNHQ", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37104445", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V271", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8N752-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YCRGLRFEEVPDYMYLRQLF", "down_seq": "ILFRTLNHQYDYTFDWTMLK", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "13", "chr_pos": "37104412", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R282", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8N752-1.271.271", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RKIGSGSFGDVYLGITTTNG", "down_seq": "DVAVKLESQKVKHPQLLYES", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "13", "chr_pos": "37105136", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E41", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8N752-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8N752-1.42.42", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N752-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q8N752-1", "length": 337, "uniprot_id": "KC1AL_HUMAN", "protein_name": "Casein kinase I isoform alpha-like", "refseq_ac": "NP_660204", "refseq_name": "casein kinase I isoform alpha-like", "gene_name": "CSNK1A1L", "gene_names_uniprotkb": "CSNK1A1L", "gene_names_refseq": "CK1; CSNK1A1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N752", "url": "https://www.uniprot.org/uniprotkb/Q8N752" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N752", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KIGSGSFGDVYLGITTTNGE", "down_seq": "VAVKLESQKVKHPQLLYESK", "snv": [ { "evidence": [ { "id": "Q8N752", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N752" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37105131", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D42", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "12", "end_pos": "12" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8N752-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8N752-1.41.41", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TD94-1.189.189", "start_pos": 189, "end_pos": 189, "uniprot_canonical_ac": "Q8TD94-1", "length": 323, "uniprot_id": "KLF14_HUMAN", "protein_name": "Krueppel-like factor 14", "refseq_ac": "NP_619638", "refseq_name": "Krueppel-like factor 14", "gene_name": "KLF14", "gene_names_uniprotkb": "KLF14; BTEB5", "gene_names_refseq": "BTEB5; KLF14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TD94", "url": "https://www.uniprot.org/uniprotkb/Q8TD94" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs781831902", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781831902", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781831902", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781831902", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781831902", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781831902#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781831902", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781831902", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GALGAGPAPAADQAPRRRSV", "down_seq": "PAAKRHQCPFPGCTKAYYKS", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr189", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs781831902", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781831902" }, { "id": "rs781831902", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781831902" }, { "id": "rs781831902", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781831902#frequency_tab" }, { "id": "rs781831902", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781831902" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "7", "chr_pos": "130733469", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T189", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "189", "end_pos": "189" } ] }, { "type": "snv", "site_list": [ { "start_pos": "189", "end_pos": "189" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "311", "end_pos": "311" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8TD94-1.195.195", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TD94-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "Q8TD94-1", "length": 323, "uniprot_id": "KLF14_HUMAN", "protein_name": "Krueppel-like factor 14", "refseq_ac": "NP_619638", "refseq_name": "Krueppel-like factor 14", "gene_name": "KLF14", "gene_names_uniprotkb": "KLF14; BTEB5", "gene_names_refseq": "BTEB5; KLF14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TD94", "url": "https://www.uniprot.org/uniprotkb/Q8TD94" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TD94", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "PAPAADQAPRRRSVTPAAKR", "down_seq": "QCPFPGCTKAYYKSSHLKSH", "snv": [ { "evidence": [ { "id": "Q8TD94", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HQC->NQC).", "chr_id": "7", "chr_pos": "130733451", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H195", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "189", "end_pos": "189" } ] }, { "type": "snv", "site_list": [ { "start_pos": "189", "end_pos": "189" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "311", "end_pos": "311" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8TD94-1.189.189", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TD94-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q8TD94-1", "length": 323, "uniprot_id": "KLF14_HUMAN", "protein_name": "Krueppel-like factor 14", "refseq_ac": "NP_619638", "refseq_name": "Krueppel-like factor 14", "gene_name": "KLF14", "gene_names_uniprotkb": "KLF14; BTEB5", "gene_names_refseq": "BTEB5; KLF14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TD94", "url": "https://www.uniprot.org/uniprotkb/Q8TD94" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TD94", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RTHTGERPFSCDWLDCDKKF", "down_seq": "RSDELARHYRTHTGEKRFSC", "snv": [ { "evidence": [ { "id": "Q8TD94", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "130733324", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T237", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "189", "end_pos": "189" } ] }, { "type": "snv", "site_list": [ { "start_pos": "189", "end_pos": "189" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "311", "end_pos": "311" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TD94-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q8TD94-1", "length": 323, "uniprot_id": "KLF14_HUMAN", "protein_name": "Krueppel-like factor 14", "refseq_ac": "NP_619638", "refseq_name": "Krueppel-like factor 14", "gene_name": "KLF14", "gene_names_uniprotkb": "KLF14; BTEB5", "gene_names_refseq": "BTEB5; KLF14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TD94", "url": "https://www.uniprot.org/uniprotkb/Q8TD94" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TD94", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRTPRIDPPLTSEVESSASG", "down_seq": "GPGPAPSFTTCL", "snv": [ { "evidence": [ { "id": "Q8TD94", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TD94" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "130733102", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S311", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "189", "end_pos": "189" } ] }, { "type": "snv", "site_list": [ { "start_pos": "189", "end_pos": "189" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "311", "end_pos": "311" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AEPPLFPDIVELNVGGQVYV", "down_seq": "RRCTVVSVPDSLLWRMFTQQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr47", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96CX2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96CX2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96CX2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96CX2", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q96CX2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96CX2" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96CX2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96CX2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NFLEQAFDKLSESGFHMVAC", "down_seq": "STGTCAFASSTDQSEDKIWT", "snv": [ { "evidence": [ { "id": "Q96CX2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96CX2" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "13", "chr_pos": "76885265", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S295", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q96CX2-1.313.313", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763676243", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763676243", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763676243", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763676243", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763676243", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763676243", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ACSSTGTCAFASSTDQSEDK", "down_seq": "WTSYTEYVFCRE", "snv": [ { "evidence": [ { "id": "rs763676243", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763676243" }, { "id": "rs763676243", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763676243" }, { "id": "rs763676243", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763676243" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IWT->NWT).", "chr_id": "13", "chr_pos": "76885211", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I313", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q96CX2-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q96CX2-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1284081642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284081642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1284081642", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284081642#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STGTCAFASSTDQSEDKIWT", "down_seq": "YTEYVFCRE", "snv": [ { "evidence": [ { "id": "rs1284081642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284081642" }, { "id": "rs1284081642", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1284081642#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SYT->NYT).", "chr_id": "13", "chr_pos": "76885202", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S316", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q96CX2-1.313.313", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LQLVLPDYFPERSRLQREAE", "down_seq": "FELPELVRRLGAPQQPGPGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "site_lbl": "Tyr119" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96CX2-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APQQPGPGPPPSRRGVHKEG", "down_seq": "LGDELLPLGYSEPEQQEGAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "site_lbl": "Ser151" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLGDELLPLGYSEPEQQEGA", "down_seq": "AGAPSPTLELASRSPSGGAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser171" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q96CX2-1.151.151", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLPLGYSEPEQQEGASAGAP", "down_seq": "PTLELASRSPSGGAAGPLLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser176" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLGYSEPEQQEGASAGAPSP", "down_seq": "LELASRSPSGGAAGPLLTPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr178" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPEQQEGASAGAPSPTLELA", "down_seq": "RSPSGGAAGPLLTPSQSLDG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "journal": "Journal of proteome research", "date": "2008", "authors": "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "KCTD12 promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition.", "journal": "Oncogene", "date": "2017", "authors": "Zhong Y, Yang J, Xu WW, Wang Y, Zheng CC, Li B, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EQQEGASAGAPSPTLELASR", "down_seq": "PSGGAAGPLLTPSQSLDGSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" }, { "database": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ], "site_lbl": "Ser185" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q96CX2-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteomic analysis of the developing mouse brain.", "journal": "Molecular & cellular proteomics : MCP", "date": "2004", "authors": "Ballif BA, Villen J, Beausoleil SA, Schwartz D, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747" } ] }, { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "journal": "Journal of proteome research", "date": "2008", "authors": "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "KCTD12 promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition.", "journal": "Oncogene", "date": "2017", "authors": "Zhong Y, Yang J, Xu WW, Wang Y, Zheng CC, Li B, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QEGASAGAPSPTLELASRSP", "down_seq": "GGAAGPLLTPSQSLDGSRRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" }, { "database": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ], "site_lbl": "Ser187" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q96CX2-1.171.171", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96CX2-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPTLELASRSPSGGAAGPLL", "down_seq": "PSQSLDGSRRSGYITIGYRG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Thr196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q96CX2-1.176.176", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q96CX2-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.", "journal": "Science", "date": "2007", "authors": "Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLELASRSPSGGAAGPLLTP", "down_seq": "QSLDGSRRSGYITIGYRGSY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser198" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q96CX2-1.178.178", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q96CX2-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "KCTD12 promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition.", "journal": "Oncogene", "date": "2017", "authors": "Zhong Y, Yang J, Xu WW, Wang Y, Zheng CC, Li B, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELASRSPSGGAAGPLLTPSQ", "down_seq": "LDGSRRSGYITIGYRGSYTI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" }, { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" }, { "database": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ], "site_lbl": "Ser200" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96CX2-1.183.183", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q96CX2-1.204.204", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Molina H, Horn DM, Tang N, Mathivanan S, Pandey A", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSPSGGAAGPLLTPSQSLDG", "down_seq": "RRSGYITIGYRGSYTIGRDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "17287340", "url": "https://glygen.org/publication/PubMed/17287340" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser204" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q96CX2-1.185.185", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q96CX2-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q96CX2-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q96CX2-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q96CX2-1.200.200", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96CX2-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "Q96CX2-1", "length": 325, "uniprot_id": "KCD12_HUMAN", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_612453", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "KCTD12", "gene_names_uniprotkb": "KCTD12; C13orf2; KIAA1778; PFET1", "gene_names_refseq": "C13orf2; KCTD12; PFET1; PFETIN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96CX2", "url": "https://www.uniprot.org/uniprotkb/Q96CX2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "KCTD12 promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition.", "journal": "Oncogene", "date": "2017", "authors": "Zhong Y, Yang J, Xu WW, Wang Y, Zheng CC, Li B, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DAQADAKFRRVARITVCGKT", "down_seq": "LAKEVFGDTLNESRDPDRPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O14965-1", "kinase_gene_name": "AURKA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ], "site_lbl": "Ser243" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q96CX2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96CX2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "28869606", "url": "https://glygen.org/publication/PubMed/28869606" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "snv", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "316", "end_pos": "316" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "243", "end_pos": "243" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96NX5-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q96NX5-1", "length": 476, "uniprot_id": "KCC1G_HUMAN", "protein_name": "Calcium/calmodulin-dependent protein kinase type 1G", "refseq_ac": "NP_065172", "refseq_name": "calcium/calmodulin-dependent protein kinase type 1G", "gene_name": "CAMK1G", "gene_names_uniprotkb": "CAMK1G; CLICK3; VWS1", "gene_names_refseq": "CAMK1G; CLICK3; CLICKIII; VWS1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96NX5", "url": "https://www.uniprot.org/uniprotkb/Q96NX5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96NX5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HYYLVMQLVSGGELFDRILE", "down_seq": "GVYTEKDASLVIQQVLSAVK", "snv": [ { "evidence": [ { "id": "Q96NX5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "209605573", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R112", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "20", "end_pos": "20" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q96NX5-1.129.129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96NX5-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "Q96NX5-1", "length": 476, "uniprot_id": "KCC1G_HUMAN", "protein_name": "Calcium/calmodulin-dependent protein kinase type 1G", "refseq_ac": "NP_065172", "refseq_name": "calcium/calmodulin-dependent protein kinase type 1G", "gene_name": "CAMK1G", "gene_names_uniprotkb": "CAMK1G; CLICK3; VWS1", "gene_names_refseq": "CAMK1G; CLICK3; CLICKIII; VWS1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96NX5", "url": "https://www.uniprot.org/uniprotkb/Q96NX5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96NX5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ILERGVYTEKDASLVIQQVL", "down_seq": "AVKYLHENGIVHRDLKPENL", "snv": [ { "evidence": [ { "id": "Q96NX5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "209605625", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S129", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "20", "end_pos": "20" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96NX5-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96NX5-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "Q96NX5-1", "length": 476, "uniprot_id": "KCC1G_HUMAN", "protein_name": "Calcium/calmodulin-dependent protein kinase type 1G", "refseq_ac": "NP_065172", "refseq_name": "calcium/calmodulin-dependent protein kinase type 1G", "gene_name": "CAMK1G", "gene_names_uniprotkb": "CAMK1G; CLICK3; VWS1", "gene_names_refseq": "CAMK1G; CLICK3; CLICKIII; VWS1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96NX5", "url": "https://www.uniprot.org/uniprotkb/Q96NX5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96NX5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "", "down_seq": "KTFIFMEVLGSGAFSEVFLV", "snv": [ { "evidence": [ { "id": "Q96NX5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96NX5" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "209595041", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R20", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "112", "end_pos": "112" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "20", "end_pos": "20" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UNX9-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q9UNX9-1", "length": 436, "uniprot_id": "KCJ14_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 14", "refseq_ac": "NP_037480", "refseq_name": "ATP-sensitive inward rectifier potassium channel 14", "gene_name": "KCNJ14", "gene_names_uniprotkb": "KCNJ14; IRK4", "gene_names_refseq": "IRK4; KCNJ14; KIR2.4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UNX9", "url": "https://www.uniprot.org/uniprotkb/Q9UNX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UNX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GLAFWLIASLHGDLAAPPPP", "down_seq": "PCFSHVASFLAAFLFALETQ", "snv": [ { "evidence": [ { "id": "Q9UNX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "48462098", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A125", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "347", "end_pos": "347" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UNX9-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q9UNX9-1", "length": 436, "uniprot_id": "KCJ14_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 14", "refseq_ac": "NP_037480", "refseq_name": "ATP-sensitive inward rectifier potassium channel 14", "gene_name": "KCNJ14", "gene_names_uniprotkb": "KCNJ14; IRK4", "gene_names_refseq": "IRK4; KCNJ14; KIR2.4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UNX9", "url": "https://www.uniprot.org/uniprotkb/Q9UNX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UNX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EGEYIPLDHQDVDVGFDGGT", "down_seq": "RIFLVSPITIVHEIDSASPL", "snv": [ { "evidence": [ { "id": "Q9UNX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "48464256", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D264", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "347", "end_pos": "347" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9UNX9-1.269.269", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UNX9-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "Q9UNX9-1", "length": 436, "uniprot_id": "KCJ14_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 14", "refseq_ac": "NP_037480", "refseq_name": "ATP-sensitive inward rectifier potassium channel 14", "gene_name": "KCNJ14", "gene_names_uniprotkb": "KCNJ14; IRK4", "gene_names_refseq": "IRK4; KCNJ14; KIR2.4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UNX9", "url": "https://www.uniprot.org/uniprotkb/Q9UNX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UNX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PLDHQDVDVGFDGGTDRIFL", "down_seq": "SPITIVHEIDSASPLYELGR", "snv": [ { "evidence": [ { "id": "Q9UNX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "48464271", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V269", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "347", "end_pos": "347" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9UNX9-1.264.264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9UNX9-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "Q9UNX9-1", "length": 436, "uniprot_id": "KCJ14_HUMAN", "protein_name": "ATP-sensitive inward rectifier potassium channel 14", "refseq_ac": "NP_037480", "refseq_name": "ATP-sensitive inward rectifier potassium channel 14", "gene_name": "KCNJ14", "gene_names_uniprotkb": "KCNJ14; IRK4", "gene_names_refseq": "IRK4; KCNJ14; KIR2.4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UNX9", "url": "https://www.uniprot.org/uniprotkb/Q9UNX9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UNX9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WGHRFEPVLFQRGSQYEVDY", "down_seq": "HFHRTYEVPGTPVCSAKELD", "snv": [ { "evidence": [ { "id": "Q9UNX9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UNX9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "48464505", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R347", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "125", "end_pos": "125" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "347", "end_pos": "347" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "rs1169801796", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169801796", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1169801796", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169801796", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs150254912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150254912", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150254912", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150254912", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150254912", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150254912", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150254912", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150254912#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150254912", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150254912", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2017437422", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017437422", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2017437422", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017437422#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GDRLNVEVDAAPTVDLNQVL", "down_seq": "ETRSQYEALVETNRREVEQW", "glycosylation": [ { "glytoucan_ac": "G00912UN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LNVEVDAAPTVDLNQVLnETR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn226", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "rs1169801796", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169801796" }, { "id": "rs1169801796", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169801796" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->DET).", "chr_id": "17", "chr_pos": "41347135", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs150254912", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150254912" }, { "id": "rs150254912", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150254912" }, { "id": "rs150254912", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150254912" }, { "id": "rs150254912", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150254912#frequency_tab" }, { "id": "rs150254912", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150254912" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->KET).", "chr_id": "17", "chr_pos": "41347133", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2017437422", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017437422" }, { "id": "rs2017437422", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017437422#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->SET).", "chr_id": "17", "chr_pos": "41347134", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N226", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O76009-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O76009-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O76009-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "O76009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76009" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O76009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76009", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "O76009", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O76009" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "O76009-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O76009-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O76009-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O76009-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O76009-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2017437234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017437234", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2017437234", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017437234#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2017437234", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2017437234", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RLNVEVDAAPTVDLNQVLNE", "down_seq": "RSQYEALVETNRREVEQWFA", "snv": [ { "evidence": [ { "id": "rs2017437234", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017437234" }, { "id": "rs2017437234", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017437234#frequency_tab" }, { "id": "rs2017437234", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2017437234" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (TRS->NRS); n-glyco-sequon-loss (NET->NEN).", "chr_id": "17", "chr_pos": "41347128", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T228", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O76009-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O76009-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O76009-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762939306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762939306", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762939306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762939306", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762939306", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762939306#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762939306", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762939306", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YFKTIEELQQKILCSKSENA", "down_seq": "LVVQIDNAKLASDDFRTKYE", "snv": [ { "evidence": [ { "id": "rs762939306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762939306" }, { "id": "rs762939306", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762939306" }, { "id": "rs762939306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762939306#frequency_tab" }, { "id": "rs762939306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762939306" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAS).", "chr_id": "17", "chr_pos": "41349399", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R126", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "O76009-1.132.132", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ELQQKILCSKSENARLVVQI", "down_seq": "NAKLASDDFRTKYETELSLR", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "17", "chr_pos": "41349383", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D132", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O76009-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MSYSCGLPSLSC", "down_seq": "TSCSSRPCVPPSCHGCTLPG", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "41350730", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R13", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O76009-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O76009-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O76009-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O76009-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs978669798", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978669798", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs978669798", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978669798#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MSYSCGLPSLSCR", "down_seq": "SCSSRPCVPPSCHGCTLPGA", "snv": [ { "evidence": [ { "id": "rs978669798", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978669798" }, { "id": "rs978669798", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978669798#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TSC->NSC).", "chr_id": "17", "chr_pos": "41350727", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O76009-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O76009-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O76009-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O76009-1.13.13", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LCLKQNHEQEVNTLRCQLGD", "down_seq": "LNVEVDAAPTVDLNQVLNET", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41347189", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R208", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41347188", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R208", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "O76009-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O76009-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TRSQYEALVETNRREVEQWF", "down_seq": "TQTEELNKQVVSSSEQLQSY", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "41347069", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A248", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O76009-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QTEELNKQVVSSSEQLQSYQ", "down_seq": "EIIELRRTVNALEIELQAQH", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41346911", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A270", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O76009-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LNKQVVSSSEQLQSYQAEII", "down_seq": "LRRTVNALEIELQAQHNLRD", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41346900", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E274", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O76009-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O76009-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ELRRTVNALEIELQAQHNLR", "down_seq": "SLENTLTESEARYSSQLSQV", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41346665", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D294", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O76009-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1051201197", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1051201197", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1051201197", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1051201197#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1051201197", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1051201197", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CEINTYRSLLESEDCKLPSN", "down_seq": "CATTNACDKSTGPCISNPCG", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPC->NLC).", "chr_id": "17", "chr_pos": "41346222", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P371", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1051201197", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1051201197" }, { "id": "rs1051201197", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1051201197#frequency_tab" }, { "id": "rs1051201197", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1051201197" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NTC).", "chr_id": "17", "chr_pos": "41346223", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P371", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O76009-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O76009-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O76009-1.389.389", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "INTYRSLLESEDCKLPSNPC", "down_seq": "TTNACDKSTGPCISNPCGLR", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "41346217", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A373", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O76009-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O76009-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O76009-1.389.389", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2144261128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144261128", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2144261128", "url": "https://www.ensembl.org/id/rs2144261128", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLESEDCKLPSNPCATTNAC", "down_seq": "KSTGPCISNPCGLRARCGPC", "snv": [ { "evidence": [ { "id": "rs2144261128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144261128" }, { "id": "rs2144261128", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2144261128" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKS->NKS).", "chr_id": "17", "chr_pos": "41346199", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D379", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O76009-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O76009-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O76009-1.389.389", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764259366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764259366", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764259366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764259366", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764259366", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764259366#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764259366", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764259366", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SNPCATTNACDKSTGPCISN", "down_seq": "CGLRARCGPCNTFGY", "snv": [ { "evidence": [ { "id": "rs764259366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764259366" }, { "id": "rs764259366", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764259366" }, { "id": "rs764259366", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764259366#frequency_tab" }, { "id": "rs764259366", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764259366" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPC->NSC).", "chr_id": "17", "chr_pos": "41346169", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P389", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPC->NTC).", "chr_id": "17", "chr_pos": "41346169", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P389", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O76009-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "O76009-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O76009-1.379.379", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SRPCVPPSCHGCTLPGACNI", "down_seq": "ANVSNCNWFCEGSFNGSEKE", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "17", "chr_pos": "41350656", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P38", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O76009-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O76009-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs141830520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141830520", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141830520", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141830520", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs141830520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141830520", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs141830520", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141830520#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141830520", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141830520", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MS", "down_seq": "SCGLPSLSCRTSCSSRPCVP", "snv": [ { "evidence": [ { "id": "rs141830520", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141830520" }, { "id": "rs141830520", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141830520" }, { "id": "rs141830520", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141830520" }, { "id": "rs141830520", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141830520#frequency_tab" }, { "id": "rs141830520", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141830520" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YSC->NSC).", "chr_id": "17", "chr_pos": "41350761", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y3", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O76009-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O76009-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O76009-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O76009-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1289619829", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289619829", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1289619829", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289619829", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VPPSCHGCTLPGACNIPANV", "down_seq": "NCNWFCEGSFNGSEKETMQF", "snv": [ { "evidence": [ { "id": "rs1289619829", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1289619829" }, { "id": "rs1289619829", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1289619829" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SNC->NNC).", "chr_id": "17", "chr_pos": "41350643", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O76009-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O76009-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2017494979", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017494979", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2017494979", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017494979#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SCHGCTLPGACNIPANVSNC", "down_seq": "WFCEGSFNGSEKETMQFLND", "snv": [ { "evidence": [ { "id": "rs2017494979", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2017494979" }, { "id": "rs2017494979", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2017494979#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCN->NCS).", "chr_id": "17", "chr_pos": "41350634", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N45", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O76009-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O76009-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O76009-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NWFCEGSFNGSEKETMQFLN", "down_seq": "RLASYLEKVRQLERDNAELE", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "17", "chr_pos": "41350575", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D65", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O76009-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O76009-1.66.66", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O76009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs140696036", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140696036", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs140696036", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs140696036", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs140696036", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140696036", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs140696036", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140696036#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs140696036", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140696036", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WFCEGSFNGSEKETMQFLND", "down_seq": "LASYLEKVRQLERDNAELEN", "snv": [ { "evidence": [ { "id": "O76009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O76009" }, { "id": "rs140696036", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140696036" }, { "id": "rs140696036", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs140696036" }, { "id": "rs140696036", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140696036" }, { "id": "rs140696036", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140696036#frequency_tab" }, { "id": "rs140696036", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140696036" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDR->NDC).", "chr_id": "17", "chr_pos": "41350572", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R66", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O76009-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O76009-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "O76009-1", "length": 404, "uniprot_id": "KT33A_HUMAN", "protein_name": "Keratin, type I cuticular Ha3-I", "refseq_ac": "NP_004129", "refseq_name": "keratin, type I cuticular Ha3-I", "gene_name": "KRT33A", "gene_names_uniprotkb": "KRT33A; HHA3-I; HKA3A; KRTHA3A", "gene_names_refseq": "HA3I; Ha-3I; K33A; KRT33A; KRTHA3A; Krt1-3; hHa3-I", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O76009", "url": "https://www.uniprot.org/uniprotkb/O76009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763991840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763991840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763991840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763991840", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763991840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763991840", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MSYSCGLP", "down_seq": "LSCRTSCSSRPCVPPSCHGC", "snv": [ { "evidence": [ { "id": "rs763991840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763991840" }, { "id": "rs763991840", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763991840" }, { "id": "rs763991840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763991840" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SLS->NLS).", "chr_id": "17", "chr_pos": "41350742", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S9", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "226", "end_pos": "226" } ] }, { "type": "snv", "site_list": [ { "start_pos": "228", "end_pos": "228" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O76009-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O76009-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O76009-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O76009-1.14.14", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1045.1045", "start_pos": 1045, "end_pos": 1045, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CEECEDGHWGYDAEVGCQAC", "down_seq": "CSLVGSTHHRCDVVTGHCQC", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CEECEDGHWGYDAEVGCQACNCSLVGSTHHR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1045", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCS->SCS).", "chr_id": "18", "chr_pos": "7014044", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1045", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.1036.1036", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.1051.1051", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.1057.1057", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.1407.1407", "start_pos": 1407, "end_pos": 1407, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs752608336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752608336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608336", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752608336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752608336", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AGSDRGPRPLVAPCVPCSCN", "down_seq": "HSDTCDPNTGKCLNCGDNTA", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "PLVAPCVPCSCNNHSDTCDPNTGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1407", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "rs752608336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608336" }, { "id": "rs752608336", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752608336" }, { "id": "rs752608336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752608336" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHS->SHS).", "chr_id": "18", "chr_pos": "7007179", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1407", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P25391-1.1410.1410", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.1579.1579", "start_pos": 1579, "end_pos": 1579, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs542801679", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542801679", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs542801679", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs542801679", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs542801679", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542801679", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs542801679", "url": "https://www.ncbi.nlm.nih.gov/snp/rs542801679#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs542801679", "url": "http://gnomad.broadinstitute.org/awesome?query=rs542801679", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs749266333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749266333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749266333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749266333", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749266333", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749266333#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749266333", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749266333", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ECVGVLLNDLDEIGDAVLSL", "down_seq": "LTGIIPVPYGILSNLENTTK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1579", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs542801679", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542801679" }, { "id": "rs542801679", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs542801679" }, { "id": "rs542801679", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs542801679" }, { "id": "rs542801679", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs542801679#frequency_tab" }, { "id": "rs542801679", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs542801679" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->DLT).", "chr_id": "18", "chr_pos": "6997813", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000981162", "site_lbl": "N1579", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749266333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749266333" }, { "id": "rs749266333", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749266333" }, { "id": "rs749266333", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749266333#frequency_tab" }, { "id": "rs749266333", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749266333" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->SLT).", "chr_id": "18", "chr_pos": "6997812", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1579", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->TLT).", "chr_id": "18", "chr_pos": "6997812", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1579", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P25391-1.1568.1568", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.1575.1575", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.1581.1581", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1248540066", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248540066", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1248540066", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248540066#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FSPWQYYAVSDSECLSRYNI", "down_seq": "PRRGPPTYRADDEVICTSYY", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr166", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1248540066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248540066" }, { "id": "rs1248540066", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248540066#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "18", "chr_pos": "7050785", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T166", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1689.1689", "start_pos": 1689, "end_pos": 1689, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2057764031", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057764031", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057764031", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057764031#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2057764015", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057764015", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057764015", "url": "https://www.ensembl.org/id/rs2057764015", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TEIMEKTTLNQTLDEDFLLP", "down_seq": "STLQNMQQNGTSLLEIMQIR", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1689", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2057764031", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057764031" }, { "id": "rs2057764031", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057764031#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->DST).", "chr_id": "18", "chr_pos": "6992664", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1689", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->KST).", "chr_id": "18", "chr_pos": "6992662", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1689", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2057764015", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057764015" }, { "id": "rs2057764015", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057764015" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->SST).", "chr_id": "18", "chr_pos": "6992663", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1689", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1717.1717", "start_pos": 1717, "end_pos": 1717, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs759432528", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759432528", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759432528", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759432528", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759432528", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759432528", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs369790608", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369790608", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369790608", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369790608", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369790608", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369790608#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369790608", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369790608", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QNGTSLLEIMQIRDFTQLHQ", "down_seq": "ATLELKAAEDLLSQIQENYQ", "glycosylation": [ { "glytoucan_ac": "G27915IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DFTQLHQnATLELK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28622IK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DFTQLHQnATLELK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DFTQLHQnATLELK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DFTQLHQnATLELK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DFTQLHQNATLELK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1717", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs759432528", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759432528" }, { "id": "rs759432528", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759432528" }, { "id": "rs759432528", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759432528" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->KAT).", "chr_id": "18", "chr_pos": "6992578", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1717", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs369790608", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369790608" }, { "id": "rs369790608", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369790608" }, { "id": "rs369790608", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369790608#frequency_tab" }, { "id": "rs369790608", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369790608" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->SAT).", "chr_id": "18", "chr_pos": "6992579", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1717", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAT->TAT).", "chr_id": "18", "chr_pos": "6992579", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1717", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.1719.1719", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.1804.1804", "start_pos": 1804, "end_pos": 1804, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MVNANLREFSDKKLHVQEEQ", "down_seq": "LTSELIVQGRGLIDAAAAQT", "glycosylation": [ { "glytoucan_ac": "G07246CJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G16125XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G44753VC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G63041LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80479JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KLHVQEEQNLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G84225JN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G96430BV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LHVQEEQnLTSELIVQGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1804", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->ILT).", "chr_id": "18", "chr_pos": "6985612", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N1804", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->TLT).", "chr_id": "18", "chr_pos": "6985612", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1804", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 14 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 14 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 14 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 14 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 14 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 14 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.1991.1991", "start_pos": 1991, "end_pos": 1991, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs752112258", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752112258", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752112258", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752112258", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752112258", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752112258", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ELRNKTNRFQENAVEITRQT", "down_seq": "ESLLILRAIPKGIRDKGAKT", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QTNESLLILR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1991", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1991", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs752112258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752112258" }, { "id": "rs752112258", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752112258" }, { "id": "rs752112258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752112258" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->DES).", "chr_id": "18", "chr_pos": "6980557", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1991", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.1979.1979", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.1993.1993", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2038.2038", "start_pos": 2038, "end_pos": 2038, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ASQSAVSTLRDVAGLSQELL", "down_seq": "TSASLSRVNTTLRETHQLLQ", "glycosylation": [ { "glytoucan_ac": "G05962QB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G07246CJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G13131HA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G16125XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G30221QT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G35541EV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G37818NZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G39471UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G50856PC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G55132BD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G68490OW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G69521XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80479JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G82501QM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLNTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G93718GY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DVAGLSQELLnTSASLSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2038", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 28 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 28 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 28 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 28 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 28 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 28 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2047.2047", "start_pos": 2047, "end_pos": 2047, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1471033253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471033253", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1471033253", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471033253#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1471033253", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471033253", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RDVAGLSQELLNTSASLSRV", "down_seq": "TTLRETHQLLQDSTMATLLA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2047", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1471033253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471033253" }, { "id": "rs1471033253", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471033253#frequency_tab" }, { "id": "rs1471033253", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471033253" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->KTT).", "chr_id": "18", "chr_pos": "6978245", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2047", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NTT->TTT).", "chr_id": "18", "chr_pos": "6978246", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N2047", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2098.2098", "start_pos": 2098, "end_pos": 2098, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1438", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] } ], "crossref": [ { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1438", "url": "https://glyconnect.expasy.org/browser/proteins/1438", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "rs1177575992", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177575992", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1177575992", "url": "https://www.ensembl.org/id/rs1177575992", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ANLLFDRLKPLKMLEENLSR", "down_seq": "LSEIKLLISQARKQAASIKV", "glycosylation": [ { "glytoucan_ac": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G20210JR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G23294PN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G25418HZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G25451PN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G44215PV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G48584BU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G50045TK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G72398FA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G80223IX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] }, { "glytoucan_ac": "G84452RH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2098", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1438", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1438" } ] } ], "snv": [ { "evidence": [ { "id": "rs1177575992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177575992" }, { "id": "rs1177575992", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1177575992" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->ILS).", "chr_id": "18", "chr_pos": "6977779", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2098", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1177575992", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177575992" }, { "id": "rs1177575992", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1177575992" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->SLS).", "chr_id": "18", "chr_pos": "6977779", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2098", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P25391-1.2084.2084", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2099.2099", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2100.2100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 11 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 11 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 11 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 11 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 11 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 11 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2243.2243", "start_pos": 2243, "end_pos": 2243, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" }, { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1600361352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600361352", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600361352", "url": "https://www.ensembl.org/id/rs1600361352", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NQKSPTKTSKSPGTANVLDV", "down_seq": "NSTLMFVGGLGGQIKKSPAV", "glycosylation": [ { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G07755XJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVnNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2243", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" } ] } ], "snv": [ { "evidence": [ { "id": "rs1600361352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600361352" }, { "id": "rs1600361352", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600361352" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->DNS).", "chr_id": "18", "chr_pos": "6973104", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2243", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P25391-1.2244.2244", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2245.2245", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.2246.2246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 13 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 12 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 12 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 12 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 12 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 12 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2244.2244", "start_pos": 2244, "end_pos": 2244, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs1276957345", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276957345", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1276957345", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1276957345", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs552970379", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552970379", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs552970379", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs552970379", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs552970379", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552970379", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs552970379", "url": "https://www.ncbi.nlm.nih.gov/snp/rs552970379#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs552970379", "url": "http://gnomad.broadinstitute.org/awesome?query=rs552970379", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QKSPTKTSKSPGTANVLDVN", "down_seq": "STLMFVGGLGGQIKKSPAVK", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SPGTANVLDVNNSTLMFVGGLGGQIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2244", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "rs1276957345", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276957345" }, { "id": "rs1276957345", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1276957345" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->DST).", "chr_id": "18", "chr_pos": "6973101", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2244", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs552970379", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552970379" }, { "id": "rs552970379", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs552970379" }, { "id": "rs552970379", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs552970379" }, { "id": "rs552970379", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs552970379#frequency_tab" }, { "id": "rs552970379", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs552970379" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->SST).", "chr_id": "18", "chr_pos": "6973100", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2244", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->TST).", "chr_id": "18", "chr_pos": "6973100", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N2244", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P25391-1.2243.2243", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2245.2245", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2246.2246", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P25391-1.2264.2264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2384.2384", "start_pos": 2384, "end_pos": 2384, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2144016609", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144016609", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2144016609", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2144016609", "database": "1000Genomes", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KVMTDLGSGPITLLTDRRYN", "down_seq": "GTWYKIAFQRNRKQGVLAVI", "glycosylation": [ { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YNnGTWYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YNnGTWYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YNnGTWYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YNnGTWYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YNNGTWYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2384", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs2144016609", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144016609" }, { "id": "rs2144016609", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2144016609" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->TGT).", "chr_id": "18", "chr_pos": "6965332", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2384", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.2386.2386", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2408.2408", "start_pos": 2408, "end_pos": 2408, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2057624969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057624969", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057624969", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057624969#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YKIAFQRNRKQGVLAVIDAY", "down_seq": "TSNKETKQGETPGASSDLNR", "glycosylation": [ { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27126ED", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G46691LC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KQGVLAVIDAYNTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QGVLAVIDAYnTSNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2408", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "snv": [ { "evidence": [ { "id": "rs2057624969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057624969" }, { "id": "rs2057624969", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057624969#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->STS).", "chr_id": "18", "chr_pos": "6964776", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2408", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.2410.2410", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.2412.2412", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.2420.2420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 14 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 14 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 14 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 14 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 14 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 14 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2619.2619", "start_pos": 2619, "end_pos": 2619, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LDENNPVEMKLGTLVESRTI", "down_seq": "VSNLYVGGIPEGEGTSLLTM", "glycosylation": [ { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TInVSNLYVGGIPEGEGTSLLTMR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2619", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.2604.2604", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.2615.2615", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2617.2617", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2621.2621", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2852.2852", "start_pos": 2852, "end_pos": 2852, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs374227019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374227019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374227019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374227019", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374227019", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374227019#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374227019", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374227019", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VEGLFYLGGLPSQYQARKIG", "down_seq": "ITHSIPACIGDVTVNSKQLD", "glycosylation": [ { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIGNITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G88891KO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "IGnITHSIPACIGDVTVNSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2852", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs374227019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374227019" }, { "id": "rs374227019", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374227019" }, { "id": "rs374227019", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374227019#frequency_tab" }, { "id": "rs374227019", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374227019" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->TIT).", "chr_id": "18", "chr_pos": "6949102", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2852", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.2854.2854", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.2863.2863", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 9 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 8 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2915.2915", "start_pos": 2915, "end_pos": 2915, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FDGSGYAALVKEGYKVQSDV", "down_seq": "ITLEFRTSSQNGVLLGISTA", "glycosylation": [ { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VQSDVnITLEFR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2915", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VQSDVnITLEFR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2915", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VQSDVNITLEFR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2915", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIT->SIT).", "chr_id": "18", "chr_pos": "6947263", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N2915", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.2899.2899", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2917.2917", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2983.2983", "start_pos": 2983, "end_pos": 2983, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2057508005", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057508005", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057508005", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057508005#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AYEPKTATVLCDGKWHTLQA", "down_seq": "KSKHRITLIVDGNAVGAESP", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "WHTLQANK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn2983", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "rs2057508005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057508005" }, { "id": "rs2057508005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057508005#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKS->IKS).", "chr_id": "18", "chr_pos": "6943299", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N2983", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKS->KKS).", "chr_id": "18", "chr_pos": "6943298", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N2983", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKS->TKS).", "chr_id": "18", "chr_pos": "6943299", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N2983", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P25391-1.2988.2988", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.2995.2995", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2058188574", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2058188574", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2058188574", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2058188574#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RQRGLFPAILNLASNAHIST", "down_seq": "ATCGEKGPEMFCKLVEHVPG", "glycosylation": [ { "glytoucan_ac": "G24193ZC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLFPAILNLASNAHISTNATCGEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn38", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "rs2058188574", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2058188574" }, { "id": "rs2058188574", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2058188574#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->SAT).", "chr_id": "18", "chr_pos": "7080406", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N38", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.25.25", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1568041333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568041333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1568041333", "url": "https://www.ensembl.org/id/rs1568041333", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SPRKIPSQQDALGGRHQVSI", "down_seq": "NTAVMQRLAPKYYWAAPEAY", "glycosylation": [ { "glytoucan_ac": "G01485JJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSINNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86182NS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G95177YH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HQVSInNTAVMQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn555", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs1568041333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568041333" }, { "id": "rs1568041333", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1568041333" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNT->SNT).", "chr_id": "18", "chr_pos": "7037651", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N555", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P25391-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.557.557", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 23 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 22 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 22 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 22 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 22 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 22 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.665.665", "start_pos": 665, "end_pos": 665, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780966401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780966401", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780966401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780966401", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780966401", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780966401#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780966401", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780966401", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FQDFHSKRQIDRDQLMTVLA", "down_seq": "VTHLLIRANYNSAKMALYRL", "glycosylation": [ { "glytoucan_ac": "G15664MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QIDRDQLMTVLAnVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G31309XD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QIDRDQLMTVLAnVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QIDRDQLMTVLAnVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QIDRDQLMTVLAnVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QIDRDQLMTVLAnVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DQLMTVLANVTHLLIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn665", "evidence": [ { "id": "P25391", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P25391#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs780966401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780966401" }, { "id": "rs780966401", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780966401" }, { "id": "rs780966401", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780966401#frequency_tab" }, { "id": "rs780966401", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780966401" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVT->SVT).", "chr_id": "18", "chr_pos": "7034536", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N665", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.667.667", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.674.674", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.676.676", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P25391-1.678.678", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.784.784", "start_pos": 784, "end_pos": 784, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TTGVHCEQCLPGFYGEPSRG", "down_seq": "PGDCQPCACPLTIASNNFSP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr784", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.952.952", "start_pos": 952, "end_pos": 952, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs766001239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766001239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766001239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766001239", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766001239", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766001239#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs766001239", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766001239", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs576734629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576734629", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs576734629", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs576734629", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs576734629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576734629", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs576734629", "url": "https://www.ncbi.nlm.nih.gov/snp/rs576734629#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs576734629", "url": "http://gnomad.broadinstitute.org/awesome?query=rs576734629", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CDQCLHGYYGLDSGHGCRPC", "down_seq": "CSVAGSVSDGCTDEGQCHCV", "glycosylation": [ { "glytoucan_ac": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "PCNCSVAGSVSDGCTDEGQCHCVPGVAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn952", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "rs766001239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766001239" }, { "id": "rs766001239", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766001239" }, { "id": "rs766001239", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766001239#frequency_tab" }, { "id": "rs766001239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766001239" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCS->DCS).", "chr_id": "18", "chr_pos": "7016626", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N952", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs576734629", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576734629" }, { "id": "rs576734629", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs576734629" }, { "id": "rs576734629", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576734629" }, { "id": "rs576734629", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs576734629#frequency_tab" }, { "id": "rs576734629", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs576734629" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCS->KCS).", "chr_id": "18", "chr_pos": "7016624", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N952", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.933.933", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.946.946", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.955.955", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "P25391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P25391" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "P25391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P25391" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P25391", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P25391", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "P25391", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P25391" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2245.2245", "start_pos": 2245, "end_pos": 2245, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2510835402", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2510835402", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057665702", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057665702", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057665702", "url": "https://www.ensembl.org/id/rs2057665702", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSPTKTSKSPGTANVLDVNN", "down_seq": "TLMFVGGLGGQIKKSPAVKV", "snv": [ { "evidence": [ { "id": "rs2510835402", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2510835402" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NST->NPT); n-glyco-sequon-loss (NNS->NNP).", "chr_id": "18", "chr_pos": "6973098", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2245", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2057665702", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057665702" }, { "id": "rs2057665702", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057665702" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->NN*).", "chr_id": "18", "chr_pos": "6973097", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2245", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.2243.2243", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2244.2244", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2246.2246", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.2264.2264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749929628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749929628", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749929628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749929628", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749929628", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749929628#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749929628", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749929628", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2058186477", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2058186477", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2058186477", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2058186477#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2058186477", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2058186477", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISHAIDGTNNWWQSPSIQNG", "down_seq": "EYHWVTITLDLRQVFQVAYV", "snv": [ { "evidence": [ { "id": "rs749929628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749929628" }, { "id": "rs749929628", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749929628" }, { "id": "rs749929628", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749929628#frequency_tab" }, { "id": "rs749929628", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749929628" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGS).", "chr_id": "18", "chr_pos": "7080014", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R102", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2058186477", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2058186477" }, { "id": "rs2058186477", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2058186477#frequency_tab" }, { "id": "rs2058186477", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2058186477" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGT).", "chr_id": "18", "chr_pos": "7080015", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R102", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1036.1036", "start_pos": 1036, "end_pos": 1036, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "CPPHTQGVKCEECEDGHWGY", "down_seq": "AEVGCQACNCSLVGSTHHRC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7015742", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1036", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P25391-1.1045.1045", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P25391-1.1051.1051", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1051.1051", "start_pos": 1051, "end_pos": 1051, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GHWGYDAEVGCQACNCSLVG", "down_seq": "THHRCDVVTGHCQCKSKFGG", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7014026", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1051", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.1036.1036", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.1045.1045", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.1057.1057", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1057.1057", "start_pos": 1057, "end_pos": 1057, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AEVGCQACNCSLVGSTHHRC", "down_seq": "VVTGHCQCKSKFGGRACDQC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7014009", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1057", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.1045.1045", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.1051.1051", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.1075.1075", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1075.1075", "start_pos": 1075, "end_pos": 1075, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750355560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750355560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750355560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750355560", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750355560", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750355560#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750355560", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750355560", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RCDVVTGHCQCKSKFGGRAC", "down_seq": "QCSLGYRDFPDCVPCDCDLR", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs750355560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750355560" }, { "id": "rs750355560", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750355560" }, { "id": "rs750355560", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750355560#frequency_tab" }, { "id": "rs750355560", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750355560" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DQC->NQC).", "chr_id": "18", "chr_pos": "7013955", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1075", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.1057.1057", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.1085.1085", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1085.1085", "start_pos": 1085, "end_pos": 1085, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CKSKFGGRACDQCSLGYRDF", "down_seq": "DCVPCDCDLRGTSGDACNLE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7013925", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P1085", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P25391-1.1075.1075", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.1097.1097", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1097.1097", "start_pos": 1097, "end_pos": 1097, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CSLGYRDFPDCVPCDCDLRG", "down_seq": "SGDACNLEQGLCGCVEETGA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "7013888", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1097", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.1085.1085", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1206.1206", "start_pos": 1206, "end_pos": 1206, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NLRGTTEGVYYQAPDFLLDA", "down_seq": "TVRQHIRAEPFYWRLPQQFQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "7011371", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1206", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1241.1241", "start_pos": 1241, "end_pos": 1241, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LPQQFQGDQLMAYGGKLKYS", "down_seq": "AFYSLDGVGTSNFEPQVLIK", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "7010352", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V1241", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1294.1294", "start_pos": 1294, "end_pos": 1294, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "APAPENGVRQEQEVAMRENF", "down_seq": "KYFNSVSEKPVTREDFMSVL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7009358", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W1294", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1337.1337", "start_pos": 1337, "end_pos": 1337, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748845224", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748845224", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748845224", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748845224", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748845224", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748845224#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748845224", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748845224", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IEYILIKASYGQGLQQSRIS", "down_seq": "ISMEVGRKAEKLHPEEEVAS", "snv": [ { "evidence": [ { "id": "rs748845224", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748845224" }, { "id": "rs748845224", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748845224" }, { "id": "rs748845224", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748845224#frequency_tab" }, { "id": "rs748845224", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748845224" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "18", "chr_pos": "7008601", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1337", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1367.1367", "start_pos": 1367, "end_pos": 1367, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EKLHPEEEVASLLENCVCPP", "down_seq": "TVGFSCQDCAPGYHRGKLPA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7008510", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1367", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P25391-1.1379.1379", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2144202750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144202750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2144202750", "url": "https://www.ensembl.org/id/rs2144202750", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "VFQVAYVIIKAANAPRPGNW", "down_seq": "LERSLDGTTFSPWQYYAVSD", "snv": [ { "evidence": [ { "id": "rs2144202750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144202750" }, { "id": "rs2144202750", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2144202750" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWI->NWT).", "chr_id": "18", "chr_pos": "7050875", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1379.1379", "start_pos": 1379, "end_pos": 1379, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LENCVCPPGTVGFSCQDCAP", "down_seq": "YHRGKLPAGSDRGPRPLVAP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "7007264", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1379", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.1367.1367", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1410.1410", "start_pos": 1410, "end_pos": 1410, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057836007", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057836007", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057836007", "url": "https://www.ensembl.org/id/rs2057836007", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DRGPRPLVAPCVPCSCNNHS", "down_seq": "TCDPNTGKCLNCGDNTAGDH", "snv": [ { "evidence": [ { "id": "rs2057836007", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057836007" }, { "id": "rs2057836007", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057836007" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTC->NTC).", "chr_id": "18", "chr_pos": "7007171", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1410", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P25391-1.1407.1407", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.1429.1429", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1424.1424", "start_pos": 1424, "end_pos": 1424, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs984433837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs984433837", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs984433837", "url": "https://www.ncbi.nlm.nih.gov/snp/rs984433837#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs984433837", "url": "http://gnomad.broadinstitute.org/awesome?query=rs984433837", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SCNNHSDTCDPNTGKCLNCG", "down_seq": "NTAGDHCDVCTSGYYGKVTG", "snv": [ { "evidence": [ { "id": "rs984433837", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs984433837" }, { "id": "rs984433837", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs984433837#frequency_tab" }, { "id": "rs984433837", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs984433837" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNT->NNT).", "chr_id": "18", "chr_pos": "7002376", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1424", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.1407.1407", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P25391-1.1410.1410", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P25391-1.1429.1429", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.1443.1443", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1427.1427", "start_pos": 1427, "end_pos": 1427, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NHSDTCDPNTGKCLNCGDNT", "down_seq": "GDHCDVCTSGYYGKVTGSAS", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "18", "chr_pos": "7002367", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1427", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.1407.1407", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P25391-1.1410.1410", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P25391-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.1429.1429", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.1443.1443", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P25391-1.1447.1447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1429.1429", "start_pos": 1429, "end_pos": 1429, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200862963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200862963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200862963", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200862963", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200862963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200862963", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200862963", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200862963#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200862963", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200862963", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SDTCDPNTGKCLNCGDNTAG", "down_seq": "HCDVCTSGYYGKVTGSASDC", "snv": [ { "evidence": [ { "id": "rs200862963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200862963" }, { "id": "rs200862963", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200862963" }, { "id": "rs200862963", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200862963" }, { "id": "rs200862963", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200862963#frequency_tab" }, { "id": "rs200862963", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200862963" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DHC->NHC).", "chr_id": "18", "chr_pos": "7002361", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "D1429", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.1410.1410", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P25391-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.1443.1443", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.1447.1447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1443.1443", "start_pos": 1443, "end_pos": 1443, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779041274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779041274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779041274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779041274", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779041274", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779041274#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779041274", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779041274", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GDNTAGDHCDVCTSGYYGKV", "down_seq": "GSASDCALCACPHSPPASFS", "snv": [ { "evidence": [ { "id": "rs779041274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779041274" }, { "id": "rs779041274", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779041274" }, { "id": "rs779041274", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779041274#frequency_tab" }, { "id": "rs779041274", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779041274" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TGS->NGS).", "chr_id": "18", "chr_pos": "7002318", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1443", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.1424.1424", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P25391-1.1429.1429", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.1447.1447", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.1461.1461", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1447.1447", "start_pos": 1447, "end_pos": 1447, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1348028612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348028612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1348028612", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1348028612#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1348028612", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348028612", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AGDHCDVCTSGYYGKVTGSA", "down_seq": "DCALCACPHSPPASFSPTCV", "snv": [ { "evidence": [ { "id": "rs1348028612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348028612" }, { "id": "rs1348028612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1348028612#frequency_tab" }, { "id": "rs1348028612", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1348028612" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SDC->NDC).", "chr_id": "18", "chr_pos": "7002306", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1447", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.1427.1427", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P25391-1.1429.1429", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.1443.1443", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.1461.1461", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1461.1461", "start_pos": 1461, "end_pos": 1461, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1420617546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1420617546", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1420617546", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1420617546#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1420617546", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1420617546", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVTGSASDCALCACPHSPPA", "down_seq": "FSPTCVLEGDHDFRCDACLL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs1420617546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1420617546" }, { "id": "rs1420617546", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1420617546#frequency_tab" }, { "id": "rs1420617546", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1420617546" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SFS->NFS).", "chr_id": "18", "chr_pos": "7002264", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1461", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.1443.1443", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P25391-1.1447.1447", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1540.1540", "start_pos": 1540, "end_pos": 1540, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs373453681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373453681", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373453681", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373453681", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs373453681", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373453681", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373453681", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373453681#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373453681", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373453681", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DCDRTSGQCVCRLGASGLRC", "down_seq": "ECEPRHILMETDCVSCDDEC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs373453681", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373453681" }, { "id": "rs373453681", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373453681" }, { "id": "rs373453681", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373453681" }, { "id": "rs373453681", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373453681#frequency_tab" }, { "id": "rs373453681", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373453681" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DEC->NEC).", "chr_id": "18", "chr_pos": "6999490", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1540", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P25391-1.1558.1558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1558.1558", "start_pos": 1558, "end_pos": 1558, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750166147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750166147", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750166147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750166147", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750166147", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750166147#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750166147", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750166147", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RCDECEPRHILMETDCVSCD", "down_seq": "ECVGVLLNDLDEIGDAVLSL", "snv": [ { "evidence": [ { "id": "rs750166147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750166147" }, { "id": "rs750166147", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750166147" }, { "id": "rs750166147", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750166147#frequency_tab" }, { "id": "rs750166147", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750166147" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DEC->NEC).", "chr_id": "18", "chr_pos": "6997876", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1558", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.1540.1540", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.1568.1568", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.1575.1575", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1568.1568", "start_pos": 1568, "end_pos": 1568, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1215376956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1215376956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1215376956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1215376956", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LMETDCVSCDDECVGVLLND", "down_seq": "DEIGDAVLSLNLTGIIPVPY", "snv": [ { "evidence": [ { "id": "rs1215376956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1215376956" }, { "id": "rs1215376956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1215376956" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDL->NDS).", "chr_id": "18", "chr_pos": "6997845", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L1568", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P25391-1.1558.1558", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.1575.1575", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.1579.1579", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P25391-1.1581.1581", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1575.1575", "start_pos": 1575, "end_pos": 1575, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SCDDECVGVLLNDLDEIGDA", "down_seq": "LSLNLTGIIPVPYGILSNLE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "6997825", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V1575", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.1558.1558", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.1568.1568", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.1579.1579", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.1581.1581", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1581.1581", "start_pos": 1581, "end_pos": 1581, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs148171853", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148171853", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148171853", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148171853#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148171853", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148171853", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VGVLLNDLDEIGDAVLSLNL", "down_seq": "GIIPVPYGILSNLENTTKYL", "snv": [ { "evidence": [ { "id": "rs148171853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853" }, { "id": "rs148171853", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853" }, { "id": "rs148171853", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148171853#frequency_tab" }, { "id": "rs148171853", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148171853" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLA).", "chr_id": "18", "chr_pos": "6997807", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1581", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs148171853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853" }, { "id": "rs148171853", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148171853" }, { "id": "rs148171853", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148171853#frequency_tab" }, { "id": "rs148171853", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148171853" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLP).", "chr_id": "18", "chr_pos": "6997807", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1581", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.1568.1568", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.1575.1575", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.1579.1579", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1626.1626", "start_pos": 1626, "end_pos": 1626, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKENMQKDLGKIKLEGVAEE", "down_seq": "DNLQKKLTRMLASTQKVNRA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6995376", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1626", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "P25391-1.1646.1646", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1646.1646", "start_pos": 1646, "end_pos": 1646, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1189820186", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1189820186", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1189820186", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1189820186#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1189820186", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1189820186", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TDNLQKKLTRMLASTQKVNR", "down_seq": "TERIFKESQDLAIAIERLQM", "snv": [ { "evidence": [ { "id": "rs1189820186", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1189820186" }, { "id": "rs1189820186", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1189820186#frequency_tab" }, { "id": "rs1189820186", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1189820186" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRT).", "chr_id": "18", "chr_pos": "6993713", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1646", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.1626.1626", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1691.1691", "start_pos": 1691, "end_pos": 1691, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs529739104", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs529739104", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529739104", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs529739104", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs529739104", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529739104", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1276475292", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276475292", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1276475292", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1276475292", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IMEKTTLNQTLDEDFLLPNS", "down_seq": "LQNMQQNGTSLLEIMQIRDF", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs529739104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104" }, { "id": "rs529739104", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529739104" }, { "id": "rs529739104", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104" }, { "id": "rs529739104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529739104" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->NSA).", "chr_id": "18", "chr_pos": "6992658", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T1691", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1276475292", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276475292" }, { "id": "rs1276475292", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1276475292" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NSI).", "chr_id": "18", "chr_pos": "6992657", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1691", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs529739104", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104" }, { "id": "rs529739104", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529739104" }, { "id": "rs529739104", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529739104" }, { "id": "rs529739104", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529739104" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NSP).", "chr_id": "18", "chr_pos": "6992658", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T1691", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.1689.1689", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1719.1719", "start_pos": 1719, "end_pos": 1719, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776426862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426862", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776426862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426862", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776426862", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776426862", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GTSLLEIMQIRDFTQLHQNA", "down_seq": "LELKAAEDLLSQIQENYQKP", "snv": [ { "evidence": [ { "id": "rs776426862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426862" }, { "id": "rs776426862", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426862" }, { "id": "rs776426862", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776426862" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->NAN).", "chr_id": "18", "chr_pos": "6992573", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1719", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.1717.1717", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1772.1772", "start_pos": 1772, "end_pos": 1772, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "HVLSKHNNELKAAEALVREA", "down_seq": "AKMQESNHLLLMVNANLREF", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "6986200", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "E1772", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1826.1826", "start_pos": 1826, "end_pos": 1826, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TSELIVQGRGLIDAAAAQTD", "down_seq": "VQDALEHLEDHQDKLLLWSA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6985546", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1826", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1866.1866", "start_pos": 1866, "end_pos": 1866, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AKIRHHIDDLVMHMSQRNAV", "down_seq": "LVYRAEDHAAEFQRLADVLY", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6985301", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1866", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1909.1909", "start_pos": 1909, "end_pos": 1909, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199766289", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199766289", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199766289", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199766289", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199766289", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199766289", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199766289", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199766289#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199766289", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199766289", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LENIRNVSLNATSAAYVHYN", "down_seq": "QSLIEESEELARDAHRTVTE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs199766289", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199766289" }, { "id": "rs199766289", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199766289" }, { "id": "rs199766289", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199766289" }, { "id": "rs199766289", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199766289#frequency_tab" }, { "id": "rs199766289", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199766289" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (IQS->NQS).", "chr_id": "18", "chr_pos": "6983169", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I1909", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P25391-1.1924.1924", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1924.1924", "start_pos": 1924, "end_pos": 1924, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YVHYNIQSLIEESEELARDA", "down_seq": "RTVTETSLLSESLVSNGKAA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HRT->NRT).", "chr_id": "18", "chr_pos": "6983125", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H1924", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.1909.1909", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.1942.1942", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1942.1942", "start_pos": 1942, "end_pos": 1942, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779172478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779172478", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779172478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779172478", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779172478", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779172478#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779172478", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779172478", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DAHRTVTETSLLSESLVSNG", "down_seq": "AAVQRSSRFLKEGNNLSRKL", "snv": [ { "evidence": [ { "id": "rs779172478", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779172478" }, { "id": "rs779172478", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779172478" }, { "id": "rs779172478", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779172478#frequency_tab" }, { "id": "rs779172478", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779172478" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGK->NGT).", "chr_id": "18", "chr_pos": "6982562", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1942", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.1924.1924", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P25391-1.1947.1947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1947.1947", "start_pos": 1947, "end_pos": 1947, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VTETSLLSESLVSNGKAAVQ", "down_seq": "SSRFLKEGNNLSRKLPGIAL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "6982547", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1947", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P25391-1.1942.1942", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1979.1979", "start_pos": 1979, "end_pos": 1979, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SRKLPGIALELSELRNKTNR", "down_seq": "QENAVEITRQTNESLLILRA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRF->NRC).", "chr_id": "18", "chr_pos": "6980592", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F1979", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P25391-1.1991.1991", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.1993.1993", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.1993.1993", "start_pos": 1993, "end_pos": 1993, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763090349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763090349", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763090349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763090349", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763090349", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763090349#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763090349", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763090349", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764149276", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764149276", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764149276", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764149276", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764149276", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764149276#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764149276", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764149276", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RNKTNRFQENAVEITRQTNE", "down_seq": "LLILRAIPKGIRDKGAKTKE", "snv": [ { "evidence": [ { "id": "rs763090349", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763090349" }, { "id": "rs763090349", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763090349" }, { "id": "rs763090349", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763090349#frequency_tab" }, { "id": "rs763090349", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763090349" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->NEL).", "chr_id": "18", "chr_pos": "6980550", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1993", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764149276", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764149276" }, { "id": "rs764149276", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764149276" }, { "id": "rs764149276", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764149276#frequency_tab" }, { "id": "rs764149276", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764149276" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->NEP).", "chr_id": "18", "chr_pos": "6980551", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1993", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P25391-1.1979.1979", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.1991.1991", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2030.2030", "start_pos": 2030, "end_pos": 2030, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KTKELATSASQSAVSTLRDV", "down_seq": "GLSQELLNTSASLSRVNTTL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "6978297", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A2030", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2040.2040", "start_pos": 2040, "end_pos": 2040, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs1568015483", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568015483", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1568015483", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1568015483#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1600366432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600366432", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600366432", "url": "https://www.ensembl.org/id/rs1600366432", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSAVSTLRDVAGLSQELLNT", "down_seq": "ASLSRVNTTLRETHQLLQDS", "snv": [ { "evidence": [ { "id": "rs1568015483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568015483" }, { "id": "rs1568015483", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1568015483#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTF).", "chr_id": "18", "chr_pos": "6978267", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2040", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1600366432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600366432" }, { "id": "rs1600366432", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600366432" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTP).", "chr_id": "18", "chr_pos": "6978268", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2040", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser2040" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2042.2042", "start_pos": 2042, "end_pos": 2042, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs758849761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758849761", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758849761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758849761", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758849761", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758849761#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AVSTLRDVAGLSQELLNTSA", "down_seq": "LSRVNTTLRETHQLLQDSTM", "snv": [ { "evidence": [ { "id": "rs758849761", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758849761" }, { "id": "rs758849761", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758849761" }, { "id": "rs758849761", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758849761#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SLS->NLS).", "chr_id": "18", "chr_pos": "6978261", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2042", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser2042" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.2049.2049", "start_pos": 2049, "end_pos": 2049, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750722310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750722310", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750722310", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750722310", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750722310", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750722310", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VAGLSQELLNTSASLSRVNT", "down_seq": "LRETHQLLQDSTMATLLAGR", "snv": [ { "evidence": [ { "id": "rs750722310", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750722310" }, { "id": "rs750722310", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750722310" }, { "id": "rs750722310", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750722310" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->NTA).", "chr_id": "18", "chr_pos": "6978241", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2049", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P25391-1.2039.2039", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2084.2084", "start_pos": 2084, "end_pos": 2084, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TLLAGRKVKDVEIQANLLFD", "down_seq": "LKPLKMLEENLSRNLSEIKL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6977822", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2084", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P25391-1.2098.2098", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P25391-1.2099.2099", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.2100.2100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2099.2099", "start_pos": 2099, "end_pos": 2099, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1179443970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179443970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1179443970", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179443970", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NLLFDRLKPLKMLEENLSRN", "down_seq": "SEIKLLISQARKQAASIKVA", "snv": [ { "evidence": [ { "id": "rs1179443970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179443970" }, { "id": "rs1179443970", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179443970" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NPS).", "chr_id": "18", "chr_pos": "6977776", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L2099", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.2084.2084", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2098.2098", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2100.2100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2100.2100", "start_pos": 2100, "end_pos": 2100, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776084401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776084401", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776084401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776084401", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776084401", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776084401", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLFDRLKPLKMLEENLSRNL", "down_seq": "EIKLLISQARKQAASIKVAV", "snv": [ { "evidence": [ { "id": "rs776084401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776084401" }, { "id": "rs776084401", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776084401" }, { "id": "rs776084401", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776084401" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NL*).", "chr_id": "18", "chr_pos": "6977773", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2100", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.2084.2084", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2098.2098", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2099.2099", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs532162048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532162048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs532162048", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs532162048", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs532162048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532162048", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs532162048", "url": "http://gnomad.broadinstitute.org/awesome?query=rs532162048", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VPLEHGEIHTSLINGRPSAD", "down_seq": "LSPKLLEFTSARYIRLRLQR", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs532162048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532162048" }, { "id": "rs532162048", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs532162048" }, { "id": "rs532162048", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532162048" }, { "id": "rs532162048", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs532162048" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "18", "chr_pos": "7049218", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D210", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2160.2160", "start_pos": 2160, "end_pos": 2160, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1270217504", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1270217504", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1270217504", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1270217504#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTLTLNVKTQEPDNLLFYLG", "down_seq": "STASDFLAVEMRRGRVAFLW", "snv": [ { "evidence": [ { "id": "rs1270217504", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1270217504" }, { "id": "rs1270217504", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1270217504#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "18", "chr_pos": "6975947", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2213.2213", "start_pos": 2213, "end_pos": 2213, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057666352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057666352", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057666352", "url": "https://www.ensembl.org/id/rs2057666352", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DFPIDDNRWHSIHVARFGNI", "down_seq": "SLSVKEMSSNQKSPTKTSKS", "snv": [ { "evidence": [ { "id": "rs2057666352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057666352" }, { "id": "rs2057666352", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057666352" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIG->NIS).", "chr_id": "18", "chr_pos": "6973194", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G2213", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2246.2246", "start_pos": 2246, "end_pos": 2246, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1600361335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600361335", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600361335", "url": "https://www.ensembl.org/id/rs1600361335", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPTKTSKSPGTANVLDVNNS", "down_seq": "LMFVGGLGGQIKKSPAVKVT", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs1600361335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600361335" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->NSA).", "chr_id": "18", "chr_pos": "6973095", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T2246", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1600361335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600361335" }, { "id": "rs1600361335", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600361335" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NSP).", "chr_id": "18", "chr_pos": "6973095", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2246", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P25391-1.2243.2243", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2244.2244", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2245.2245", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.2264.2264", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RPSADDLSPKLLEFTSARYI", "down_seq": "LRLQRIRTLNADLMTLSHRE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049172", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R225", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2264.2264", "start_pos": 2264, "end_pos": 2264, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762095728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762095728", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762095728", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762095728", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762095728", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762095728", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NSTLMFVGGLGGQIKKSPAV", "down_seq": "VTHFKGCLGEAFLNGKSIGL", "snv": [ { "evidence": [ { "id": "rs762095728", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762095728" }, { "id": "rs762095728", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762095728" }, { "id": "rs762095728", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762095728" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVT->NVT).", "chr_id": "18", "chr_pos": "6971964", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K2264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.2244.2244", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P25391-1.2245.2245", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P25391-1.2246.2246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "PSADDLSPKLLEFTSARYIR", "down_seq": "RLQRIRTLNADLMTLSHREP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049170", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L226", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SADDLSPKLLEFTSARYIRL", "down_seq": "LQRIRTLNADLMTLSHREPK", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049166", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R227", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2288.2288", "start_pos": 2288, "end_pos": 2288, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774822926", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774822926", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774822926", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774822926", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774822926", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774822926", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FKGCLGEAFLNGKSIGLWNY", "down_seq": "EREGKCRGCFGSSQNEDPSF", "snv": [ { "evidence": [ { "id": "rs774822926", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774822926" }, { "id": "rs774822926", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774822926" }, { "id": "rs774822926", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774822926" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYI->NYT).", "chr_id": "18", "chr_pos": "6971893", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I2288", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DLSPKLLEFTSARYIRLRLQ", "down_seq": "IRTLNADLMTLSHREPKELD", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "3", "frequency": "0.4", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049158", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R230", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2312.2312", "start_pos": 2312, "end_pos": 2312, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GKCRGCFGSSQNEDPSFHFD", "down_seq": "SGYSVVEKSLPATVTQIIML", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6966263", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G2312", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2335.2335", "start_pos": 2335, "end_pos": 2335, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373670761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373670761", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373670761", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373670761", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs373670761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373670761", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373670761", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373670761#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373670761", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373670761", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YSVVEKSLPATVTQIIMLFN", "down_seq": "FSPNGLLLYLGSYGTKDFLS", "snv": [ { "evidence": [ { "id": "rs373670761", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373670761" }, { "id": "rs373670761", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373670761" }, { "id": "rs373670761", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373670761" }, { "id": "rs373670761", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373670761#frequency_tab" }, { "id": "rs373670761", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373670761" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TFS->NFS).", "chr_id": "18", "chr_pos": "6966193", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T2335", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P25391-1.2336.2336", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2336.2336", "start_pos": 2336, "end_pos": 2336, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780045907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780045907", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780045907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780045907", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780045907", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780045907", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SVVEKSLPATVTQIIMLFNT", "down_seq": "SPNGLLLYLGSYGTKDFLSI", "snv": [ { "evidence": [ { "id": "rs780045907", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780045907" }, { "id": "rs780045907", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780045907" }, { "id": "rs780045907", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780045907" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTF->NTS).", "chr_id": "18", "chr_pos": "6966190", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F2336", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P25391-1.2335.2335", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2360.2360", "start_pos": 2360, "end_pos": 2360, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GLLLYLGSYGTKDFLSIELF", "down_seq": "GRVKVMTDLGSGPITLLTDR", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "18", "chr_pos": "6965405", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2360", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2386.2386", "start_pos": 2386, "end_pos": 2386, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751693129", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751693129", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751693129", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751693129", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751693129", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751693129", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MTDLGSGPITLLTDRRYNNG", "down_seq": "WYKIAFQRNRKQGVLAVIDA", "snv": [ { "evidence": [ { "id": "rs751693129", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751693129" }, { "id": "rs751693129", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751693129" }, { "id": "rs751693129", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751693129" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->NGI).", "chr_id": "18", "chr_pos": "6965326", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2386", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.2384.2384", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750730687", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750730687", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750730687", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750730687", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750730687", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750730687#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750730687", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750730687", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SARYIRLRLQRIRTLNADLM", "down_seq": "LSHREPKELDPIVTRRYYYS", "snv": [ { "evidence": [ { "id": "rs750730687", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750730687" }, { "id": "rs750730687", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750730687" }, { "id": "rs750730687", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750730687#frequency_tab" }, { "id": "rs750730687", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750730687" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TLS->NLS).", "chr_id": "18", "chr_pos": "7049127", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.256.256", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2410.2410", "start_pos": 2410, "end_pos": 2410, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779169278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779169278", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779169278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779169278", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779169278", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779169278#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779169278", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779169278", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1208557200", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208557200", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1208557200", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208557200#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1208557200", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208557200", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IAFQRNRKQGVLAVIDAYNT", "down_seq": "NKETKQGETPGASSDLNRLD", "snv": [ { "evidence": [ { "id": "rs779169278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779169278" }, { "id": "rs779169278", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779169278" }, { "id": "rs779169278", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779169278#frequency_tab" }, { "id": "rs779169278", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779169278" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTG).", "chr_id": "18", "chr_pos": "6964771", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2410", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1208557200", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208557200" }, { "id": "rs1208557200", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208557200#frequency_tab" }, { "id": "rs1208557200", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208557200" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTI).", "chr_id": "18", "chr_pos": "6964770", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2410", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1208557200", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208557200" }, { "id": "rs1208557200", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208557200#frequency_tab" }, { "id": "rs1208557200", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1208557200" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTS->NTN).", "chr_id": "18", "chr_pos": "6964770", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2410", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.2408.2408", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2412.2412", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.2420.2420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2412.2412", "start_pos": 2412, "end_pos": 2412, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057624878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057624878", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057624878", "url": "https://www.ensembl.org/id/rs2057624878", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FQRNRKQGVLAVIDAYNTSN", "down_seq": "ETKQGETPGASSDLNRLDKD", "snv": [ { "evidence": [ { "id": "rs2057624878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057624878" }, { "id": "rs2057624878", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057624878" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KET->NET).", "chr_id": "18", "chr_pos": "6964763", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K2412", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P25391-1.2408.2408", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2410.2410", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P25391-1.2420.2420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2420.2420", "start_pos": 2420, "end_pos": 2420, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VLAVIDAYNTSNKETKQGET", "down_seq": "GASSDLNRLDKDPIYVGGLP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6964740", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P2420", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.2408.2408", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P25391-1.2410.2410", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P25391-1.2412.2412", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IRLRLQRIRTLNADLMTLSH", "down_seq": "EPKELDPIVTRRYYYSIKDI", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049115", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R244", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "7049116", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R244", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.225.225", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P25391-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P25391-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P25391-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2475.2475", "start_pos": 2475, "end_pos": 2475, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762327413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762327413", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762327413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762327413", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762327413", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762327413#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762327413", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762327413", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VGCIKNLEISRSTFDLLRNS", "down_seq": "GVRKGCLLEPIRSVSFLKGG", "snv": [ { "evidence": [ { "id": "rs762327413", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762327413" }, { "id": "rs762327413", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762327413" }, { "id": "rs762327413", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762327413#frequency_tab" }, { "id": "rs762327413", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762327413" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSY->NSC).", "chr_id": "18", "chr_pos": "6961973", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y2475", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P25391-1.2479.2479", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P25391-1.2488.2488", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2479.2479", "start_pos": 2479, "end_pos": 2479, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KNLEISRSTFDLLRNSYGVR", "down_seq": "GCLLEPIRSVSFLKGGYIEL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KGC->NGC).", "chr_id": "18", "chr_pos": "6961960", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K2479", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P25391-1.2475.2475", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.2488.2488", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2488.2488", "start_pos": 2488, "end_pos": 2488, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057608807", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057608807", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057608807", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057608807#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FDLLRNSYGVRKGCLLEPIR", "down_seq": "VSFLKGGYIELPPKSLSPES", "snv": [ { "evidence": [ { "id": "rs2057608807", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057608807" }, { "id": "rs2057608807", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057608807#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "18", "chr_pos": "6961749", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2488", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.2475.2475", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.2479.2479", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2562.2562", "start_pos": 2562, "end_pos": 2562, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs772910533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772910533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772910533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772910533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772910533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772910533", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs772910533", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772910533", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VPFFSVMLIGGNIEVHVNPG", "down_seq": "GTGLRKALLHAPTGTCSDGQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs772910533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772910533" }, { "id": "rs772910533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772910533" }, { "id": "rs772910533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772910533" }, { "id": "rs772910533", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772910533" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "18", "chr_pos": "6959435", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D2562", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ADLMTLSHREPKELDPIVTR", "down_seq": "YYYSIKDISVGGMCICYGHA", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7049080", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R256", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2593.2593", "start_pos": 2593, "end_pos": 2593, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1318849133", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318849133", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1318849133", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1318849133#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "APTGTCSDGQAHSISLVRNR", "down_seq": "IITVQLDENNPVEMKLGTLV", "snv": [ { "evidence": [ { "id": "rs1318849133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318849133" }, { "id": "rs1318849133", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1318849133#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRS).", "chr_id": "18", "chr_pos": "6958662", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R2593", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P25391-1.2604.2604", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VLLVLLLCVAAQCRQRGLFP", "down_seq": "ILNLASNAHISTNATCGEKG", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "10", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient count (10/4177).", "chr_id": "18", "chr_pos": "7080446", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A25", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P25391-1.38.38", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2604.2604", "start_pos": 2604, "end_pos": 2604, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1422576225", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1422576225", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1422576225", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1422576225#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1422576225", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1422576225", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HSISLVRNRRIITVQLDENN", "down_seq": "VEMKLGTLVESRTINVSNLY", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNS).", "chr_id": "18", "chr_pos": "6958631", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P2604", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1422576225", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1422576225" }, { "id": "rs1422576225", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1422576225#frequency_tab" }, { "id": "rs1422576225", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1422576225" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNT).", "chr_id": "18", "chr_pos": "6958631", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P2604", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P25391-1.2593.2593", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.2615.2615", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P25391-1.2617.2617", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P25391-1.2619.2619", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.2621.2621", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2615.2615", "start_pos": 2615, "end_pos": 2615, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ITVQLDENNPVEMKLGTLVE", "down_seq": "RTINVSNLYVGGIPEGEGTS", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SRT->NRT).", "chr_id": "18", "chr_pos": "6958597", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S2615", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P25391-1.2604.2604", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2617.2617", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.2619.2619", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.2621.2621", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2617.2617", "start_pos": 2617, "end_pos": 2617, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VQLDENNPVEMKLGTLVESR", "down_seq": "INVSNLYVGGIPEGEGTSLL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6958591", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T2617", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.2604.2604", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2615.2615", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.2619.2619", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.2621.2621", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2621.2621", "start_pos": 2621, "end_pos": 2621, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ENNPVEMKLGTLVESRTINV", "down_seq": "NLYVGGIPEGEGTSLLTMRR", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVF).", "chr_id": "18", "chr_pos": "6958579", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S2621", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.2604.2604", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.2615.2615", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.2617.2617", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2619.2619", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HREPKELDPIVTRRYYYSIK", "down_seq": "ISVGGMCICYGHASSCPWDE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "18", "chr_pos": "7046349", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D263", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.244.244", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.256.256", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2747.2747", "start_pos": 2747, "end_pos": 2747, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PFNQSAVRKKLSVELSIRTF", "down_seq": "SSGLIYYMAHQNQADYAVLQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6950940", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A2747", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2772.2772", "start_pos": 2772, "end_pos": 2772, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IYYMAHQNQADYAVLQLHGG", "down_seq": "LHFMFDLGKGRTKVSHPALL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "6950864", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R2772", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P25391-1.2779.2779", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2779.2779", "start_pos": 2779, "end_pos": 2779, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NQADYAVLQLHGGRLHFMFD", "down_seq": "GKGRTKVSHPALLSDGKWHT", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6950844", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L2779", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P25391-1.2772.2772", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2854.2854", "start_pos": 2854, "end_pos": 2854, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1600339797", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600339797", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600339797", "url": "https://www.ensembl.org/id/rs1600339797", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GLFYLGGLPSQYQARKIGNI", "down_seq": "HSIPACIGDVTVNSKQLDKD", "snv": [ { "evidence": [ { "id": "rs1600339797", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600339797" }, { "id": "rs1600339797", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600339797" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->NIP).", "chr_id": "18", "chr_pos": "6948553", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2854", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.2852.2852", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.2863.2863", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2863.2863", "start_pos": 2863, "end_pos": 2863, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs137948858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137948858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs137948858", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs137948858", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs137948858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137948858", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs137948858", "url": "https://www.ncbi.nlm.nih.gov/snp/rs137948858#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs137948858", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137948858", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SQYQARKIGNITHSIPACIG", "down_seq": "VTVNSKQLDKDSPVSAFTVN", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs137948858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137948858" }, { "id": "rs137948858", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs137948858" }, { "id": "rs137948858", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137948858" }, { "id": "rs137948858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs137948858#frequency_tab" }, { "id": "rs137948858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137948858" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "18", "chr_pos": "6948526", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D2863", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P25391-1.2852.2852", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.2854.2854", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2899.2899", "start_pos": 2899, "end_pos": 2899, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AFTVNRCYAVAQEGTYFDGS", "down_seq": "YAALVKEGYKVQSDVNITLE", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6948418", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G2899", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P25391-1.2915.2915", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.2917.2917", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2917.2917", "start_pos": 2917, "end_pos": 2917, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376554656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376554656", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GSGYAALVKEGYKVQSDVNI", "down_seq": "LEFRTSSQNGVLLGISTAKV", "snv": [ { "evidence": [ { "id": "rs376554656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376554656" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->NII).", "chr_id": "18", "chr_pos": "6947257", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2917", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.2899.2899", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.2915.2915", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2953.2953", "start_pos": 2953, "end_pos": 2953, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "STAKVDAIGLELVDGKVLFH", "down_seq": "NNGAGRITAAYEPKTATVLC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6943389", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "V2953", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P25391-1.2956.2956", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2956.2956", "start_pos": 2956, "end_pos": 2956, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1600336029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600336029", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600336029", "url": "https://www.ensembl.org/id/rs1600336029", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KVDAIGLELVDGKVLFHVNN", "down_seq": "AGRITAAYEPKTATVLCDGK", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNG->NNC).", "chr_id": "18", "chr_pos": "6943381", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G2956", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1600336029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600336029" }, { "id": "rs1600336029", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600336029" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNG->NNS).", "chr_id": "18", "chr_pos": "6943381", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G2956", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P25391-1.2953.2953", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2988.2988", "start_pos": 2988, "end_pos": 2988, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TATVLCDGKWHTLQANKSKH", "down_seq": "ITLIVDGNAVGAESPHTQST", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6943284", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R2988", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P25391-1.2983.2983", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.2995.2995", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2995.2995", "start_pos": 2995, "end_pos": 2995, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GKWHTLQANKSKHRITLIVD", "down_seq": "NAVGAESPHTQSTSVDTNNP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6943264", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G2995", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.2983.2983", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.2988.2988", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.3032.3032", "start_pos": 3032, "end_pos": 3032, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1568000139", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568000139", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1568000139", "url": "https://www.ensembl.org/id/rs1568000139", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNNPIYVGGYPAGVKQKCLR", "down_seq": "QTSFRGCLRKLALIKSPQVQ", "snv": [ { "evidence": [ { "id": "rs1568000139", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1568000139" }, { "id": "rs1568000139", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1568000139" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SQT->NQT).", "chr_id": "18", "chr_pos": "6942212", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S3032", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.3061.3061", "start_pos": 3061, "end_pos": 3061, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RKLALIKSPQVQSFDFSRAF", "down_seq": "LHGVFLHSCPGTES", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "6942126", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E3061", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RPGTVSSGNTCEACNCHNKA", "down_seq": "DCYYDESVAKQKKSLNTAGQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDC->NDC).", "chr_id": "18", "chr_pos": "7043380", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K334", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P25391-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P25391-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P25391-1.352.352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.346.346", "start_pos": 346, "end_pos": 346, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ACNCHNKAKDCYYDESVAKQ", "down_seq": "KSLNTAGQFRGGGVCINCLQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKS->NKS).", "chr_id": "18", "chr_pos": "7043344", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K346", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P25391-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P25391-1.351.351", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.352.352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs946094668", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946094668", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs946094668", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946094668#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs946094668", "url": "http://gnomad.broadinstitute.org/awesome?query=rs946094668", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KAKDCYYDESVAKQKKSLNT", "down_seq": "GQFRGGGVCINCLQNTMGIN", "snv": [ { "evidence": [ { "id": "rs946094668", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946094668" }, { "id": "rs946094668", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946094668#frequency_tab" }, { "id": "rs946094668", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs946094668" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "18", "chr_pos": "7043328", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A352", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P25391-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.351.351", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LQNTMGINCETCIDGYYRPH", "down_seq": "VSPYEDEPCRPCNCDPVGSL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KVS->NVS).", "chr_id": "18", "chr_pos": "7043227", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K385", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CKEGYTGEKCDRCQLGYKDY", "down_seq": "TCVSCGCNPVGSASDEPCTG", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "7040153", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P449", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.451.451", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.451.451", "start_pos": 451, "end_pos": 451, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "EGYTGEKCDRCQLGYKDYPT", "down_seq": "VSCGCNPVGSASDEPCTGPC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "C", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7040147", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "C451", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.449.449", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NVEGKACDRCKPGFYNLKEK", "down_seq": "PRGCSECFCFGVSDVCSSLS", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "18", "chr_pos": "7038885", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N496", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "P25391-1.510.510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.510.510", "start_pos": 510, "end_pos": 510, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YNLKEKNPRGCSECFCFGVS", "down_seq": "VCSSLSWPVGQVNSMSGWLV", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVC->NVC).", "chr_id": "18", "chr_pos": "7038845", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D510", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P25391-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P25391-1.525.525", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.524.524", "start_pos": 524, "end_pos": 524, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs748013058", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013058", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748013058", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013058", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748013058", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748013058", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FCFGVSDVCSSLSWPVGQVN", "down_seq": "MSGWLVTDLISPRKIPSQQD", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs748013058", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013058" }, { "id": "rs748013058", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013058" }, { "id": "rs748013058", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748013058" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SMS->NMS).", "chr_id": "18", "chr_pos": "7037744", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S524", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P25391-1.510.510", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.525.525", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.525.525", "start_pos": 525, "end_pos": 525, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs202033730", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202033730", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202033730", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202033730", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202033730", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202033730", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202033730", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202033730", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "CFGVSDVCSSLSWPVGQVNS", "down_seq": "SGWLVTDLISPRKIPSQQDA", "snv": [ { "evidence": [ { "id": "rs202033730", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202033730" }, { "id": "rs202033730", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202033730" }, { "id": "rs202033730", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202033730" }, { "id": "rs202033730", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202033730" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSM->NST).", "chr_id": "18", "chr_pos": "7037741", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "M525", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.510.510", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.524.524", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.548.548", "start_pos": 548, "end_pos": 548, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WLVTDLISPRKIPSQQDALG", "down_seq": "RHQVSINNTAVMQRLAPKYY", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "18", "chr_pos": "7037673", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G548", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P25391-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.555.555", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.557.557", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.549.549", "start_pos": 549, "end_pos": 549, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVTDLISPRKIPSQQDALGG", "down_seq": "HQVSINNTAVMQRLAPKYYW", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7037669", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R549", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P25391-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.555.555", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P25391-1.557.557", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.557.557", "start_pos": 557, "end_pos": 557, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745473158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745473158", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745473158", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745473158", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745473158", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745473158", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RKIPSQQDALGGRHQVSINN", "down_seq": "AVMQRLAPKYYWAAPEAYLG", "snv": [ { "evidence": [ { "id": "rs745473158", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745473158" }, { "id": "rs745473158", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745473158" }, { "id": "rs745473158", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745473158" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNT->NNI).", "chr_id": "18", "chr_pos": "7037645", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T557", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P25391-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.555.555", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.558.558", "start_pos": 558, "end_pos": 558, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs757016883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757016883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757016883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757016883", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757016883", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757016883#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757016883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757016883", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KIPSQQDALGGRHQVSINNT", "down_seq": "VMQRLAPKYYWAAPEAYLGN", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs757016883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757016883" }, { "id": "rs757016883", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757016883" }, { "id": "rs757016883", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757016883#frequency_tab" }, { "id": "rs757016883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757016883" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "18", "chr_pos": "7037643", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A558", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P25391-1.548.548", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P25391-1.555.555", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.557.557", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.590.590", "start_pos": 590, "end_pos": 590, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AAPEAYLGNKLTAFGGFLKY", "down_seq": "VSYDIPVETVDSNLMSHADV", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7036057", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T590", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P25391-1.599.599", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.600.600", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P25391-1.610.610", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.599.599", "start_pos": 599, "end_pos": 599, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KLTAFGGFLKYTVSYDIPVE", "down_seq": "VDSNLMSHADVIIKGNGLTL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7036030", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T599", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.600.600", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.610.610", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ATCGEKGPEMFCKLVEHVPG", "down_seq": "PVRNPQCRICDGNSANPRER", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "18", "chr_pos": "7080343", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R59", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "P25391-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.600.600", "start_pos": 600, "end_pos": 600, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LTAFGGFLKYTVSYDIPVET", "down_seq": "DSNLMSHADVIIKGNGLTLS", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7036028", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V600", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P25391-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.599.599", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.610.610", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FLKYTVSYDIPVETVDSNLM", "down_seq": "HADVIIKGNGLTLSTQAEGL", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7036009", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S606", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.599.599", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P25391-1.600.600", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P25391-1.622.622", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.610.610", "start_pos": 610, "end_pos": 610, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "TVSYDIPVETVDSNLMSHAD", "down_seq": "IIKGNGLTLSTQAEGLSLQP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7035998", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V610", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P25391-1.590.590", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P25391-1.599.599", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P25391-1.600.600", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P25391-1.622.622", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.622.622", "start_pos": 622, "end_pos": 622, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SNLMSHADVIIKGNGLTLST", "down_seq": "AEGLSLQPYEEYLNVVRLVP", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "7034665", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q622", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P25391-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P25391-1.610.610", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.667.667", "start_pos": 667, "end_pos": 667, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2144167055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144167055", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2144167055", "url": "https://www.ensembl.org/id/rs2144167055", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DFHSKRQIDRDQLMTVLANV", "down_seq": "HLLIRANYNSAKMALYRLES", "snv": [ { "evidence": [ { "id": "rs2144167055", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2144167055" }, { "id": "rs2144167055", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2144167055" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->NVI).", "chr_id": "18", "chr_pos": "7034530", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T667", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.665.665", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P25391-1.674.674", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.676.676", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P25391-1.678.678", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IDRDQLMTVLANVTHLLIRA", "down_seq": "YNSAKMALYRLESVSLDIAS", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7034509", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N674", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.665.665", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P25391-1.667.667", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.676.676", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P25391-1.678.678", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.676.676", "start_pos": 676, "end_pos": 676, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1274335199", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274335199", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1274335199", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1274335199#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1274335199", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274335199", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RDQLMTVLANVTHLLIRANY", "down_seq": "SAKMALYRLESVSLDIASSN", "snv": [ { "evidence": [ { "id": "rs1274335199", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274335199" }, { "id": "rs1274335199", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1274335199#frequency_tab" }, { "id": "rs1274335199", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274335199" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYN->NYS).", "chr_id": "18", "chr_pos": "7034503", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N676", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P25391-1.665.665", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.667.667", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.674.674", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P25391-1.678.678", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.678.678", "start_pos": 678, "end_pos": 678, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1275856775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275856775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1275856775", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275856775", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QLMTVLANVTHLLIRANYNS", "down_seq": "KMALYRLESVSLDIASSNAI", "snv": [ { "evidence": [ { "id": "rs1275856775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275856775" }, { "id": "rs1275856775", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275856775" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "18", "chr_pos": "7034498", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A678", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.665.665", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P25391-1.667.667", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P25391-1.674.674", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P25391-1.676.676", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.718.718", "start_pos": 718, "end_pos": 718, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2510084761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2510084761", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IDLVVAADVEHCECPQGYTG", "down_seq": "SCESCLSGYYRVDGILFGGI", "snv": [ { "evidence": [ { "id": "rs2510084761", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2510084761" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TSC->NSC).", "chr_id": "18", "chr_pos": "7032994", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T718", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs367866675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367866675", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs367866675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367866675", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs367866675", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367866675", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EHVPGRPVRNPQCRICDGNS", "down_seq": "NPRERHPISHAIDGTNNWWQ", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" }, { "id": "rs367866675", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367866675" }, { "id": "rs367866675", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367866675" }, { "id": "rs367866675", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367866675" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "18", "chr_pos": "7080299", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A74", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P25391-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.839.839", "start_pos": 839, "end_pos": 839, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143031283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143031283", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143031283", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs143031283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143031283", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143031283#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143031283", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143031283", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CAPGYSGAWCERCADGYYGN", "down_seq": "TVPGESCVPCDCSGNVDPSE", "snv": [ { "evidence": [ { "id": "rs143031283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283" }, { "id": "rs143031283", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143031283" }, { "id": "rs143031283", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283" }, { "id": "rs143031283", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143031283#frequency_tab" }, { "id": "rs143031283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143031283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NST).", "chr_id": "18", "chr_pos": "7023350", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P839", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143031283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283" }, { "id": "rs143031283", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143031283" }, { "id": "rs143031283", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143031283" }, { "id": "rs143031283", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143031283#frequency_tab" }, { "id": "rs143031283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143031283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NTT).", "chr_id": "18", "chr_pos": "7023350", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P839", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P25391-1.844.844", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P25391-1.853.853", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.844.844", "start_pos": 844, "end_pos": 844, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SGAWCERCADGYYGNPTVPG", "down_seq": "SCVPCDCSGNVDPSEAGHCD", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7023335", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E844", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P25391-1.839.839", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.853.853", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.853.853", "start_pos": 853, "end_pos": 853, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DGYYGNPTVPGESCVPCDCS", "down_seq": "NVDPSEAGHCDSVTGECLKC", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "18", "chr_pos": "7023308", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G853", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P25391-1.839.839", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P25391-1.844.844", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.900.900", "start_pos": 900, "end_pos": 900, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201104095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201104095", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201104095", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201104095", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201104095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201104095", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201104095", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201104095#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201104095", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201104095", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AHCERCADGFYGDAVTAKNC", "down_seq": "ACECHVKGSHSAVCHLETGL", "snv": [ { "evidence": [ { "id": "rs201104095", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201104095" }, { "id": "rs201104095", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201104095" }, { "id": "rs201104095", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201104095" }, { "id": "rs201104095", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201104095#frequency_tab" }, { "id": "rs201104095", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201104095" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCR->NCC).", "chr_id": "18", "chr_pos": "7023167", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R900", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.933.933", "start_pos": 933, "end_pos": 933, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751582070", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751582070", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751582070", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751582070", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751582070", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751582070", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VCHLETGLCDCKPNVTGQQC", "down_seq": "QCLHGYYGLDSGHGCRPCNC", "snv": [ { "evidence": [ { "id": "rs751582070", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751582070" }, { "id": "rs751582070", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751582070" }, { "id": "rs751582070", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751582070" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DQC->NQC).", "chr_id": "18", "chr_pos": "7017289", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D933", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "P25391-1.946.946", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P25391-1.952.952", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1247026416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247026416", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1247026416", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1247026416#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1247026416", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247026416", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "SANPRERHPISHAIDGTNNW", "down_seq": "QSPSIQNGREYHWVTITLDL", "snv": [ { "evidence": [ { "id": "rs1247026416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1247026416" }, { "id": "rs1247026416", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1247026416#frequency_tab" }, { "id": "rs1247026416", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1247026416" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NWW->NWC).", "chr_id": "18", "chr_pos": "7080041", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W93", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P25391-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.946.946", "start_pos": 946, "end_pos": 946, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369361438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369361438", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369361438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369361438", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369361438", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369361438#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369361438", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369361438", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "NVTGQQCDQCLHGYYGLDSG", "down_seq": "GCRPCNCSVAGSVSDGCTDE", "snv": [ { "evidence": [ { "id": "rs369361438", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369361438" }, { "id": "rs369361438", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369361438" }, { "id": "rs369361438", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369361438#frequency_tab" }, { "id": "rs369361438", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369361438" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGC->NGC).", "chr_id": "18", "chr_pos": "7016644", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H946", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P25391-1.933.933", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P25391-1.952.952", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P25391-1.955.955", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.955.955", "start_pos": 955, "end_pos": 955, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "CLHGYYGLDSGHGCRPCNCS", "down_seq": "AGSVSDGCTDEGQCHCVPGV", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "18", "chr_pos": "7016617", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V955", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.946.946", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P25391-1.952.952", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.992.992", "start_pos": 992, "end_pos": 992, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P25391", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VPGVAGKRCDRCAHGFYAYQ", "down_seq": "GSCTPCDCPHTQNTCDPETG", "snv": [ { "evidence": [ { "id": "P25391", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P25391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "18", "chr_pos": "7016506", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D992", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P25391-1.994.994", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.994.994", "start_pos": 994, "end_pos": 994, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs927113647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927113647", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs927113647", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927113647#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs927113647", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927113647", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GVAGKRCDRCAHGFYAYQDG", "down_seq": "CTPCDCPHTQNTCDPETGEC", "snv": [ { "evidence": [ { "id": "rs927113647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs927113647" }, { "id": "rs927113647", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs927113647#frequency_tab" }, { "id": "rs927113647", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs927113647" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SCT->NCT).", "chr_id": "18", "chr_pos": "7016499", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S994", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P25391-1.992.992", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P25391-1.2039.2039", "start_pos": 2039, "end_pos": 2039, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SQSAVSTLRDVAGLSQELLN", "down_seq": "SASLSRVNTTLRETHQLLQD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr2039" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P25391-1.2030.2030", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P25391-1.2038.2038", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.2040.2040", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P25391-1.2042.2042", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P25391-1.2047.2047", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P25391-1.2049.2049", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P25391-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "P25391-1", "length": 3075, "uniprot_id": "LAMA1_HUMAN", "protein_name": "Laminin subunit alpha-1", "refseq_ac": "NP_005550", "refseq_name": "laminin subunit alpha-1 precursor", "gene_name": "LAMA1", "gene_names_uniprotkb": "LAMA1; LAMA", "gene_names_refseq": "LAMA1; LAMA; PTBHS; S-LAM-alpha", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P25391", "url": "https://www.uniprot.org/uniprotkb/P25391" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NKAKDCYYDESVAKQKKSLN", "down_seq": "AGQFRGGGVCINCLQNTMGI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P25391", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P25391" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr351" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "2038", "end_pos": "2038" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "2619", "end_pos": "2619" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "784", "end_pos": "784" }, { "start_pos": "952", "end_pos": "952" } ] }, { "type": "snv", "site_list": [ { "start_pos": "2245", "end_pos": "2245" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "1036", "end_pos": "1036" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "1051", "end_pos": "1051" }, { "start_pos": "1057", "end_pos": "1057" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1097", "end_pos": "1097" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1241", "end_pos": "1241" }, { "start_pos": "1294", "end_pos": "1294" }, { "start_pos": "1337", "end_pos": "1337" }, { "start_pos": "1367", "end_pos": "1367" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "1379", "end_pos": "1379" }, { "start_pos": "1407", "end_pos": "1407" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "1424", "end_pos": "1424" }, { "start_pos": "1427", "end_pos": "1427" }, { "start_pos": "1429", "end_pos": "1429" }, { "start_pos": "1443", "end_pos": "1443" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1558", "end_pos": "1558" }, { "start_pos": "1568", "end_pos": "1568" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1579", "end_pos": "1579" }, { "start_pos": "1581", "end_pos": "1581" }, { "start_pos": "1626", "end_pos": "1626" }, { "start_pos": "1646", "end_pos": "1646" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "1689", "end_pos": "1689" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1717", "end_pos": "1717" }, { "start_pos": "1719", "end_pos": "1719" }, { "start_pos": "1772", "end_pos": "1772" }, { "start_pos": "1804", "end_pos": "1804" }, { "start_pos": "1826", "end_pos": "1826" }, { "start_pos": "1866", "end_pos": "1866" }, { "start_pos": "1909", "end_pos": "1909" }, { "start_pos": "1924", "end_pos": "1924" }, { "start_pos": "1942", "end_pos": "1942" }, { "start_pos": "1947", "end_pos": "1947" }, { "start_pos": "1979", "end_pos": "1979" }, { "start_pos": "1991", "end_pos": "1991" }, { "start_pos": "1993", "end_pos": "1993" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "2047", "end_pos": "2047" }, { "start_pos": "2049", "end_pos": "2049" }, { "start_pos": "2084", "end_pos": "2084" }, { "start_pos": "2098", "end_pos": "2098" }, { "start_pos": "2099", "end_pos": "2099" }, { "start_pos": "2100", "end_pos": "2100" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2160", "end_pos": "2160" }, { "start_pos": "2213", "end_pos": "2213" }, { "start_pos": "2243", "end_pos": "2243" }, { "start_pos": "2244", "end_pos": "2244" }, { "start_pos": "2246", "end_pos": "2246" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "2264", "end_pos": "2264" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "2288", "end_pos": "2288" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "2312", "end_pos": "2312" }, { "start_pos": "2335", "end_pos": "2335" }, { "start_pos": "2336", "end_pos": "2336" }, { "start_pos": "2360", "end_pos": "2360" }, { "start_pos": "2384", "end_pos": "2384" }, { "start_pos": "2386", "end_pos": "2386" }, { "start_pos": "2408", "end_pos": "2408" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "2410", "end_pos": "2410" }, { "start_pos": "2412", "end_pos": "2412" }, { "start_pos": "2420", "end_pos": "2420" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "2475", "end_pos": "2475" }, { "start_pos": "2479", "end_pos": "2479" }, { "start_pos": "2488", "end_pos": "2488" }, { "start_pos": "2562", "end_pos": "2562" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "2593", "end_pos": "2593" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "2604", "end_pos": "2604" }, { "start_pos": "2615", "end_pos": "2615" }, { "start_pos": "2617", "end_pos": "2617" }, { "start_pos": "2621", "end_pos": "2621" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "2747", "end_pos": "2747" }, { "start_pos": "2772", "end_pos": "2772" }, { "start_pos": "2779", "end_pos": "2779" }, { "start_pos": "2852", "end_pos": "2852" }, { "start_pos": "2854", "end_pos": "2854" }, { "start_pos": "2863", "end_pos": "2863" }, { "start_pos": "2899", "end_pos": "2899" }, { "start_pos": "2915", "end_pos": "2915" }, { "start_pos": "2917", "end_pos": "2917" }, { "start_pos": "2953", "end_pos": "2953" }, { "start_pos": "2956", "end_pos": "2956" }, { "start_pos": "2983", "end_pos": "2983" }, { "start_pos": "2988", "end_pos": "2988" }, { "start_pos": "2995", "end_pos": "2995" }, { "start_pos": "3032", "end_pos": "3032" }, { "start_pos": "3061", "end_pos": "3061" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "548", "end_pos": "548" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "590", "end_pos": "590" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "600", "end_pos": "600" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "622", "end_pos": "622" }, { "start_pos": "665", "end_pos": "665" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "676", "end_pos": "676" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "839", "end_pos": "839" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "853", "end_pos": "853" }, { "start_pos": "900", "end_pos": "900" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "946", "end_pos": "946" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "992", "end_pos": "992" }, { "start_pos": "994", "end_pos": "994" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2039", "end_pos": "2039" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2042", "end_pos": "2042" }, { "start_pos": "351", "end_pos": "351" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P25391-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P25391-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P25391-1.352.352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P49862-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CGQPNDPGVYTQVCKFTKWI", "down_seq": "DTMKKHR", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn246", "evidence": [ { "id": "P49862", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P49862#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P49862-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P49862-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P49862-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBalpha complex.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Berthier A, Vinod M, Porez G, Steenackers A, Alexandre J, Yamakawa N, Gheeraert C, Ploton M, Marechal X, Dubois-Chevalier J, Hovasse A, Schaeffer-Reiss C, Cianferani S, Rolando C, Bray F, Duez H, Eeckhoute J, Lefebvre T, Staels B, Lefebvre P", "evidence": [ { "database": "O-GlcNAc Database", "id": "P49862", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P49862" } ], "reference": [ { "type": "PubMed", "id": "30397120", "url": "https://glygen.org/publication/PubMed/30397120" } ] } ], "crossref": [ { "id": "30397120", "url": "https://glygen.org/publication/PubMed/30397120", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P49862", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P49862", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "P49862", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P49862" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P49862-1.19.19", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P49862-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Chymotryptic specificity determinants in the 1.0 A structure of the zinc-inhibited human tissue kallikrein 7.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Debela M, Hess P, Magdolen V, Schechter NM, Steiner T, Huber R, Bode W, Goettig P", "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "reference": [ { "type": "PubMed", "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180" } ] } ], "crossref": [ { "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RAQRIKASKSFRHPGYSTQT", "down_seq": "VNDLMLVKLNSQARLSSMVK", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "No zinc inhibition.", "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" }, { "database": "PubMed", "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P49862-1.100.100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P49862-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Chymotryptic specificity determinants in the 1.0 A structure of the zinc-inhibited human tissue kallikrein 7.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Debela M, Hess P, Magdolen V, Schechter NM, Steiner T, Huber R, Bode W, Goettig P", "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "reference": [ { "type": "PubMed", "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180" } ] } ], "crossref": [ { "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "APCARGSHPWQVALLSGNQL", "down_seq": "CGGVLVNERWVLTAAHCKMN", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "F", "comment": "No effect on zinc inhibition.", "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" }, { "database": "PubMed", "id": "17909180", "url": "https://glygen.org/publication/PubMed/17909180" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P49862-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P49862-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGSDTLGDRRAQRIKASKSF", "down_seq": "HPGYSTQTHVNDLMLVKLNS", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "50980411", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R100", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P49862-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P49862-1.109.109", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2091067657", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2091067657", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2091067657", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2091067657#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SSMVKKVRLPSRCEPPGTTC", "down_seq": "VSGWGTTTSPDVTFPSDLMC", "snv": [ { "evidence": [ { "id": "rs2091067657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2091067657" }, { "id": "rs2091067657", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2091067657#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TVS->NVS).", "chr_id": "19", "chr_pos": "50980275", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P49862-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RLPSRCEPPGTTCTVSGWGT", "down_seq": "TSPDVTFPSDLMCVDVKLIS", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TTS->NTS).", "chr_id": "19", "chr_pos": "50980254", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T152", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P49862-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1487065339", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1487065339", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1487065339", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1487065339#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1487065339", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1487065339", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VKLISPQDCTKVYKDLLENS", "down_seq": "LCAGIPDSKKNACNGDSGGP", "snv": [ { "evidence": [ { "id": "rs1487065339", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1487065339" }, { "id": "rs1487065339", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1487065339#frequency_tab" }, { "id": "rs1487065339", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1487065339" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSM->NST).", "chr_id": "19", "chr_pos": "50979831", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M188", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "P49862-1.196.196", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MARSLLLPLQILLLSLAL", "down_seq": "TAGEEAQGDKIIDGAPCARG", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "12", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient count (12/4484).", "chr_id": "19", "chr_pos": "50982345", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E19", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P49862-1.0.0", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GIPDSKKNACNGDSGGPLVC", "down_seq": "GTLQGLVSWGTFPCGQPNDP", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "19", "chr_pos": "50977662", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R212", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P49862-1.196.196", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P49862-1.232.232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RGTLQGLVSWGTFPCGQPND", "down_seq": "GVYTQVCKFTKWINDTMKKH", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDP->NDT).", "chr_id": "19", "chr_pos": "50977604", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P232", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P49862-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P49862-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P49862-1.246.246", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P49862-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760820716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760820716", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760820716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760820716", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760820716", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760820716#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760820716", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760820716", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SWGTFPCGQPNDPGVYTQVC", "down_seq": "FTKWINDTMKKHR", "snv": [ { "evidence": [ { "id": "rs760820716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760820716" }, { "id": "rs760820716", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760820716" }, { "id": "rs760820716", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760820716#frequency_tab" }, { "id": "rs760820716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760820716" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KFT->NFT).", "chr_id": "19", "chr_pos": "50977578", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K240", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P49862-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P49862-1.246.246", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P49862-1.248.248", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774830711", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774830711", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774830711", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774830711", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774830711", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774830711#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774830711", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774830711", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPNDPGVYTQVCKFTKWIND", "down_seq": "MKKHR", "snv": [ { "evidence": [ { "id": "rs774830711", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774830711" }, { "id": "rs774830711", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774830711" }, { "id": "rs774830711", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774830711#frequency_tab" }, { "id": "rs774830711", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774830711" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->NDA).", "chr_id": "19", "chr_pos": "50977556", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T248", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P49862-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P49862-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P49862-1.246.246", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749663401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749663401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749663401", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749663401", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "WQVALLSGNQLHCGGVLVNE", "down_seq": "WVLTAAHCKMNEYTVHLGSD", "snv": [ { "evidence": [ { "id": "rs749663401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401" }, { "id": "rs749663401", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401" }, { "id": "rs749663401", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749663401" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NEC).", "chr_id": "19", "chr_pos": "50981801", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R63", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749663401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401" }, { "id": "rs749663401", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749663401" }, { "id": "rs749663401", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749663401" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NES).", "chr_id": "19", "chr_pos": "50981801", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R63", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P49862-1.54.54", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P49862", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WVLTAAHCKMNEYTVHLGSD", "down_seq": "LGDRRAQRIKASKSFRHPGY", "snv": [ { "evidence": [ { "id": "P49862", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P49862" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "50980458", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T84", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P49862-1.100.100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P49862-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P49862-1", "length": 253, "uniprot_id": "KLK7_HUMAN", "protein_name": "Kallikrein-7", "refseq_ac": "NP_001193982", "refseq_name": "kallikrein-7 isoform 2", "gene_name": "KLK7", "gene_names_uniprotkb": "KLK7; PRSS6; SCCE", "gene_names_refseq": "KLK7; PRSS6; SCCE; hK7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P49862", "url": "https://www.uniprot.org/uniprotkb/P49862" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "P49862-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P49862-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P49862", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P49862", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CTKVYKDLLENSMLCAGIPD", "down_seq": "KKNACNGDSGGPLVCRGTLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P49862", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P49862" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser196" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "246", "end_pos": "246" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "109", "end_pos": "109" }, { "start_pos": "54", "end_pos": "54" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "84", "end_pos": "84" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P49862-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P49862-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q2TBA0-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "IFTICVSFLQKRLCLSNCLA", "down_seq": "FRLGLLLDCARLAVAARDFI", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "42686024", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V136", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q2TBA0-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "CLSNCLAVFRLGLLLDCARL", "down_seq": "VAARDFICAHFTLVARDADF", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "42686063", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A149", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q2TBA0-1.136.136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.222.222", "start_pos": 222, "end_pos": 222, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AGSGDAEAQAERQRALPTVF", "down_seq": "SVRCRLLPRAFLESRVERHP", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "42686282", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E222", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELLRKVQMVKDAHEGRITTL", "down_seq": "KKKKGKDGAGAKEADKGTSK", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "42686424", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R269", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.310.310", "start_pos": 310, "end_pos": 310, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AKAEEDEEAERILPGILNDT", "down_seq": "RFGMFLQDLIFMISEEGAVA", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "42686546", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L310", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "HVSLVTKENQVFVAGGLFYN", "down_seq": "DNKEDPMSAYFLQFDHLDSE", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "42686729", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E371", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FLQFDHLDSEWLGMPPLPSP", "down_seq": "CLFGLGEALNSIYVVGGREI", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "3", "chr_pos": "42688194", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R402", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2TBA0-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "Q2TBA0-1", "length": 621, "uniprot_id": "KLH40_HUMAN", "protein_name": "Kelch-like protein 40", "refseq_ac": "NP_689606", "refseq_name": "kelch-like protein 40", "gene_name": "KLHL40", "gene_names_uniprotkb": "KLHL40; KBTBD5; SRYP", "gene_names_refseq": "KBTBD5; KLHL40; NEM8; SRYP; SYRP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2TBA0", "url": "https://www.uniprot.org/uniprotkb/Q2TBA0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2TBA0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGEALNSIYVVGGREIKDGE", "down_seq": "CLDSVMCYDRLSFKWGESDP", "snv": [ { "evidence": [ { "id": "Q2TBA0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2TBA0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "42688268", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R427", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "222", "end_pos": "222" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "427", "end_pos": "427" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6JVE9-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q6JVE9-1", "length": 175, "uniprot_id": "LCN8_HUMAN", "protein_name": "Epididymal-specific lipocalin-8", "refseq_ac": "NP_001332863", "refseq_name": "epididymal-specific lipocalin-8 isoform 1 precursor", "gene_name": "LCN8", "gene_names_uniprotkb": "LCN8; LCN5", "gene_names_refseq": "EP17; LCN5; LCN8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SLVLTAPKRVEGLFLTLSGS", "down_seq": "LTVKVAYNSSGSCEIEKIVG", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn66", "evidence": [ { "id": "Q6JVE9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "66", "end_pos": "66" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6JVE9-1.74.74", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6JVE9-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "Q6JVE9-1", "length": 175, "uniprot_id": "LCN8_HUMAN", "protein_name": "Epididymal-specific lipocalin-8", "refseq_ac": "NP_001332863", "refseq_name": "epididymal-specific lipocalin-8 isoform 1 precursor", "gene_name": "LCN8", "gene_names_uniprotkb": "LCN8; LCN5", "gene_names_refseq": "EP17; LCN5; LCN8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RVEGLFLTLSGSNLTVKVAY", "down_seq": "SSGSCEIEKIVGSEIDSTGK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn74", "evidence": [ { "id": "Q6JVE9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "66", "end_pos": "66" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6JVE9-1.66.66", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6JVE9-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6JVE9-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "Q6JVE9-1", "length": 175, "uniprot_id": "LCN8_HUMAN", "protein_name": "Epididymal-specific lipocalin-8", "refseq_ac": "NP_001332863", "refseq_name": "epididymal-specific lipocalin-8 isoform 1 precursor", "gene_name": "LCN8", "gene_names_uniprotkb": "LCN8; LCN5", "gene_names_refseq": "EP17; LCN5; LCN8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772091181", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772091181", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772091181", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772091181", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772091181", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772091181", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs772091181", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772091181", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TDYEGYAILRVSLMWRGRNF", "down_seq": "VLKYFTRSLEDKDRLGFWKF", "snv": [ { "evidence": [ { "id": "rs772091181", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772091181" }, { "id": "rs772091181", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772091181" }, { "id": "rs772091181", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772091181" }, { "id": "rs772091181", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs772091181" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFR->NFC).", "chr_id": "9", "chr_pos": "136755430", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R128", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "66", "end_pos": "66" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6JVE9-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "Q6JVE9-1", "length": 175, "uniprot_id": "LCN8_HUMAN", "protein_name": "Epididymal-specific lipocalin-8", "refseq_ac": "NP_001332863", "refseq_name": "epididymal-specific lipocalin-8 isoform 1 precursor", "gene_name": "LCN8", "gene_names_uniprotkb": "LCN8; LCN5", "gene_names_refseq": "EP17; LCN5; LCN8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6JVE9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6JVE9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs377343381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377343381", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377343381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377343381", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377343381", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377343381#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs377343381", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377343381", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs377343381", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs377343381", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SGALTAHCIGGFWREVGVAS", "down_seq": "QSLVLTAPKRVEGLFLTLSG", "snv": [ { "evidence": [ { "id": "Q6JVE9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6JVE9" }, { "id": "rs377343381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377343381" }, { "id": "rs377343381", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377343381" }, { "id": "rs377343381", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377343381#frequency_tab" }, { "id": "rs377343381", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377343381" }, { "id": "rs377343381", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs377343381" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DQS->NQS).", "chr_id": "9", "chr_pos": "136757132", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D44", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "66", "end_pos": "66" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6JVE9-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q6JVE9-1", "length": 175, "uniprot_id": "LCN8_HUMAN", "protein_name": "Epididymal-specific lipocalin-8", "refseq_ac": "NP_001332863", "refseq_name": "epididymal-specific lipocalin-8 isoform 1 precursor", "gene_name": "LCN8", "gene_names_uniprotkb": "LCN8; LCN5", "gene_names_refseq": "EP17; LCN5; LCN8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6JVE9", "url": "https://www.uniprot.org/uniprotkb/Q6JVE9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6JVE9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6JVE9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs369638208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369638208", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369638208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369638208", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369638208", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369638208#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369638208", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369638208", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs369638208", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs369638208", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KVAYNSSGSCEIEKIVGSEI", "down_seq": "STGKFAFPGHREIHVLDTDY", "snv": [ { "evidence": [ { "id": "Q6JVE9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6JVE9" }, { "id": "rs369638208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369638208" }, { "id": "rs369638208", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369638208" }, { "id": "rs369638208", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369638208#frequency_tab" }, { "id": "rs369638208", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369638208" }, { "id": "rs369638208", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs369638208" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DST->NST).", "chr_id": "9", "chr_pos": "136756549", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D90", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "66", "end_pos": "66" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "snv", "site_list": [ { "start_pos": "128", "end_pos": "128" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "90", "end_pos": "90" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6JVE9-1.74.74", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZMR3-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q6ZMR3-1", "length": 332, "uniprot_id": "LDH6A_HUMAN", "protein_name": "L-lactate dehydrogenase A-like 6A", "refseq_ac": "NP_001137543", "refseq_name": "L-lactate dehydrogenase A-like 6A", "gene_name": "LDHAL6A", "gene_names_uniprotkb": "LDHAL6A; LDHL2", "gene_names_refseq": "LDH6A; LDHAL6A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZMR3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZMR3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TDKDPEQWENVHKKVISSGY", "down_seq": "MVKMKGYTSWGISLSVADLT", "snv": [ { "evidence": [ { "id": "Q6ZMR3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZMR3" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "18477629", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E240", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "240", "end_pos": "240" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "239", "end_pos": "239" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6ZMR3-1.239.239", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZMR3-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "Q6ZMR3-1", "length": 332, "uniprot_id": "LDH6A_HUMAN", "protein_name": "L-lactate dehydrogenase A-like 6A", "refseq_ac": "NP_001137543", "refseq_name": "L-lactate dehydrogenase A-like 6A", "gene_name": "LDHAL6A", "gene_names_uniprotkb": "LDHAL6A; LDHL2", "gene_names_refseq": "LDH6A; LDHAL6A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GTDKDPEQWENVHKKVISSG", "down_seq": "EMVKMKGYTSWGISLSVADL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "site_lbl": "Tyr239" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "240", "end_pos": "240" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "239", "end_pos": "239" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6ZMR3-1.240.240", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZMR3-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "Q6ZMR3-1", "length": 332, "uniprot_id": "LDH6A_HUMAN", "protein_name": "L-lactate dehydrogenase A-like 6A", "refseq_ac": "NP_001137543", "refseq_name": "L-lactate dehydrogenase A-like 6A", "gene_name": "LDHAL6A", "gene_names_uniprotkb": "LDHAL6A; LDHL2", "gene_names_refseq": "LDH6A; LDHAL6A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LSVPCILGENGITDLIKVKL", "down_seq": "LEEEACLQKSAETLWEIQKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "site_lbl": "Thr309" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "240", "end_pos": "240" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "239", "end_pos": "239" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q6ZMR3-1.322.322", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZMR3-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "Q6ZMR3-1", "length": 332, "uniprot_id": "LDH6A_HUMAN", "protein_name": "L-lactate dehydrogenase A-like 6A", "refseq_ac": "NP_001137543", "refseq_name": "L-lactate dehydrogenase A-like 6A", "gene_name": "LDHAL6A", "gene_names_uniprotkb": "LDHAL6A; LDHL2", "gene_names_refseq": "LDH6A; LDHAL6A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DLIKVKLTLEEEACLQKSAE", "down_seq": "LWEIQKELKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZMR3", "url": "https://www.uniprot.org/uniprotkb/Q6ZMR3" } ], "site_lbl": "Thr322" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "240", "end_pos": "240" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "239", "end_pos": "239" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "322", "end_pos": "322" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6ZMR3-1.309.309", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZST4-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "Q6ZST4-1", "length": 164, "uniprot_id": "LCNL1_HUMAN", "protein_name": "Lipocalin-like 1 protein", "refseq_ac": "NP_997393", "refseq_name": "lipocalin-like 1 protein", "gene_name": "LCNL1", "gene_names_uniprotkb": "LCNL1", "gene_names_refseq": "LCNL1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZST4", "url": "https://www.uniprot.org/uniprotkb/Q6ZST4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZST4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZST4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PLGNGDLALKFGYPTPHGGC", "down_seq": "KMDTTFTEGAVPGQFSNPAM", "snv": [ { "evidence": [ { "id": "Q6ZST4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZST4" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "136984508", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q47", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z4W3-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "Q7Z4W3-1", "length": 81, "uniprot_id": "KR193_HUMAN", "protein_name": "Keratin-associated protein 19-3", "refseq_ac": "NP_853640", "refseq_name": "keratin-associated protein 19-3", "gene_name": "KRTAP19-3", "gene_names_uniprotkb": "KRTAP19-3; KAP19.3", "gene_names_refseq": "GTRHP; KAP19.3; KRTAP19-3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z4W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z4W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z4W3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YGCGGFGGLGYGYGCGCGSF", "down_seq": "RLGSGCGYGGYGYGSGFGGY", "snv": [ { "evidence": [ { "id": "Q7Z4W3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30491861", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R33", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "33", "end_pos": "33" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z4W3-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q7Z4W3-1", "length": 81, "uniprot_id": "KR193_HUMAN", "protein_name": "Keratin-associated protein 19-3", "refseq_ac": "NP_853640", "refseq_name": "keratin-associated protein 19-3", "gene_name": "KRTAP19-3", "gene_names_uniprotkb": "KRTAP19-3; KAP19.3", "gene_names_refseq": "GTRHP; KAP19.3; KRTAP19-3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z4W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z4W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z4W3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GYGYGSGFGGYGYGSGFGGY", "down_seq": "YGCYRPSYYGGYGFSGFY", "snv": [ { "evidence": [ { "id": "Q7Z4W3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "21", "chr_pos": "30491771", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G63", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "33", "end_pos": "33" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q7Z4W3-1.68.68", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z4W3-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "Q7Z4W3-1", "length": 81, "uniprot_id": "KR193_HUMAN", "protein_name": "Keratin-associated protein 19-3", "refseq_ac": "NP_853640", "refseq_name": "keratin-associated protein 19-3", "gene_name": "KRTAP19-3", "gene_names_uniprotkb": "KRTAP19-3; KAP19.3", "gene_names_refseq": "GTRHP; KAP19.3; KRTAP19-3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z4W3", "url": "https://www.uniprot.org/uniprotkb/Q7Z4W3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z4W3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SGFGGYGYGSGFGGYGYGCY", "down_seq": "PSYYGGYGFSGFY", "snv": [ { "evidence": [ { "id": "Q7Z4W3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z4W3" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "21", "chr_pos": "30491755", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R68", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "33", "end_pos": "33" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q7Z4W3-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs766364480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766364480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766364480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766364480", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766364480", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766364480#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs766364480", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766364480", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PALGANSPWNSKPPSSQESK", "down_seq": "ENPTSQASQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser402", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q86U70", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q86U70", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86U70" }, { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "snv": [ { "evidence": [ { "id": "rs766364480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766364480" }, { "id": "rs766364480", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766364480" }, { "id": "rs766364480", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766364480#frequency_tab" }, { "id": "rs766364480", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766364480" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "10", "chr_pos": "102108124", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S402", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q86U70-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q86U70-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.406.406", "start_pos": 406, "end_pos": 406, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs773354858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773354858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773354858", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773354858#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773354858", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773354858", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs773354858", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773354858", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ANSPWNSKPPSSQESKSENP", "down_seq": "SQASQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr406", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q86U70", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q86U70", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ] } ], "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" }, { "id": "rs773354858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858" }, { "id": "rs773354858", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858" }, { "id": "rs773354858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773354858#frequency_tab" }, { "id": "rs773354858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773354858" }, { "id": "rs773354858", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773354858" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "10", "chr_pos": "102108112", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T406", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs773354858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858" }, { "id": "rs773354858", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773354858" }, { "id": "rs773354858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773354858#frequency_tab" }, { "id": "rs773354858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773354858" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "10", "chr_pos": "102108112", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T406", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q86U70-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "title": "OGA mutant aberrantly hydrolyzes O-GlcNAc modification from PDLIM7 to modulate p53 and cytoskeleton in promoting cancer cell malignancy.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-06-11", "authors": "Hu Chia-Wei, Wang Ao, Fan Dacheng, Worth Matthew, Chen Zhengwei, Huang Junfeng, Xie Jinshan, Macdonald John, Li Lingjun, Jiang Jiaoyang", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38838015", "url": "https://glygen.org/publication/PubMed/38838015", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSPWNSKPPSSQESKSENPT", "down_seq": "QASQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser407", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q86U70", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q86U70", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86U70" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "38838015", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38838015" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86U70-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://oglcnac.org/atlas/detail/Q86U70", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs768226147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768226147", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768226147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768226147", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768226147", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768226147#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768226147", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768226147", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768226147", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768226147", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WNSKPPSSQESKSENPTSQA", "down_seq": "", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser410", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q86U70", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q86U70" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q86U70", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q86U70" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" }, { "id": "rs768226147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768226147" }, { "id": "rs768226147", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768226147" }, { "id": "rs768226147", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768226147#frequency_tab" }, { "id": "rs768226147", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768226147" }, { "id": "rs768226147", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768226147" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "10", "chr_pos": "102108100", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S410", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NGNAFPPFHPGTMLDRDVGP", "down_seq": "PMYPPTYLEPGIGRHTPYGN", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr45", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q86U70-1.61.61", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.245.249", "start_pos": 245, "end_pos": 249, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer.", "journal": "Cancer research", "date": "2009", "authors": "Johnsen SA, Gungor C, Prenzel T, Riethdorf S, Riethdorf L, Taniguchi-Ishigaki N, Rau T, Tursun B, Furlow JD, Sauter G, Scheffner M, Pantel K, Gannon F, Bach I", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "19117995", "url": "https://glygen.org/publication/PubMed/19117995" } ] } ], "crossref": [ { "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19117995", "url": "https://glygen.org/publication/PubMed/19117995", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "LCVIL", "start_aa": "L", "up_seq": "QLSKNITRCGLSNSTLNYLR", "down_seq": "EPMQELMSRHKTYSLSPRDC", "mutagenesis": [ { "sequence_org": "LCVIL", "sequence_mut": "ACVAA", "comment": "Abolishes interaction with ESR1.", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" }, { "database": "PubMed", "id": "19117995", "url": "https://glygen.org/publication/PubMed/19117995" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q86U70-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86U70-1.265.265", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86U70-1.267.267", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760258946", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760258946", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760258946", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760258946", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760258946", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760258946", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LRLCVILEPMQELMSRHKTY", "down_seq": "LSPRDCLKTCLFQKWQRMVA", "snv": [ { "evidence": [ { "id": "rs760258946", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760258946" }, { "id": "rs760258946", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760258946" }, { "id": "rs760258946", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760258946" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SLS->NLS).", "chr_id": "10", "chr_pos": "102109452", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q86U70-1.245.249", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86U70-1.265.265", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q86U70-1.267.267", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.267.267", "start_pos": 267, "end_pos": 267, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VILEPMQELMSRHKTYSLSP", "down_seq": "DCLKTCLFQKWQRMVAPPAE", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "102109440", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R267", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q86U70-1.245.249", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q86U70-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86U70-1.265.265", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763679443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763679443", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763679443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763679443", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763679443", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763679443#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763679443", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763679443", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KRRKRKMSGGSTMSSGGGNT", "down_seq": "NSNSKKKSPASTFALSSQVP", "snv": [ { "evidence": [ { "id": "rs763679443", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763679443" }, { "id": "rs763679443", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763679443" }, { "id": "rs763679443", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763679443#frequency_tab" }, { "id": "rs763679443", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763679443" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "10", "chr_pos": "102109090", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N315", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q86U70-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86U70-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q86U70-1.329.329", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2068212135", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2068212135", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2068212135", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2068212135#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KRKMSGGSTMSSGGGNTNNS", "down_seq": "SKKKSPASTFALSSQVPDVM", "snv": [ { "evidence": [ { "id": "rs2068212135", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2068212135" }, { "id": "rs2068212135", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2068212135#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSN->NSS).", "chr_id": "10", "chr_pos": "102109081", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N318", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86U70-1.302.302", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q86U70-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q86U70-1.329.329", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.329.329", "start_pos": 329, "end_pos": 329, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SGGGNTNNSNSKKKSPASTF", "down_seq": "LSSQVPDVMVVGEPTLMGGE", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "102109049", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A329", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q86U70-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q86U70-1.318.318", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SSQVPDVMVVGEPTLMGGEF", "down_seq": "DEDERLITRLENTQFDAANG", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "102108278", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G351", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ENTQFDAANGIDDEDSFNNS", "down_seq": "ALGANSPWNSKPPSSQESKS", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "10", "chr_pos": "102108185", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P382", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FDAANGIDDEDSFNNSPALG", "down_seq": "NSPWNSKPPSSQESKSENPT", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "10", "chr_pos": "102108173", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A386", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q86U70-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ANGIDDEDSFNNSPALGANS", "down_seq": "WNSKPPSSQESKSENPTSQA", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "10", "chr_pos": "102108164", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P389", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q86U70-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.400.400", "start_pos": 400, "end_pos": 400, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143992634", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143992634", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143992634", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143992634", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143992634", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143992634#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143992634", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143992634", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSPALGANSPWNSKPPSSQE", "down_seq": "KSENPTSQASQ", "snv": [ { "evidence": [ { "id": "rs143992634", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143992634" }, { "id": "rs143992634", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143992634" }, { "id": "rs143992634", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143992634#frequency_tab" }, { "id": "rs143992634", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143992634" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKS->NKS).", "chr_id": "10", "chr_pos": "102108130", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S400", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q86U70-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86U70-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q86U70-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1283637045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283637045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1283637045", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1283637045", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1283637045", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283637045", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GANSPWNSKPPSSQESKSEN", "down_seq": "TSQASQ", "snv": [ { "evidence": [ { "id": "rs1283637045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283637045" }, { "id": "rs1283637045", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1283637045" }, { "id": "rs1283637045", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283637045" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPT->NST).", "chr_id": "NC_000010.11", "chr_pos": "102108116", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "1e-06", "site_lbl": "P405", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q86U70-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q86U70-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q86U70-1.400.400", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q86U70-1.402.402", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q86U70-1.406.406", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86U70-1.407.407", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q86U70-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RLQNWTEECDNLWWDAFTTE", "down_seq": "FEDDAMLTITFCLEDGPKRY", "snv": [ { "evidence": [ { "id": "Q86U70", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86U70" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "102110930", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "F97", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" }, { "database": "iPTMnet", "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LCVILEPMQELMSRHKTYSL", "down_seq": "PRDCLKTCLFQKWQRMVAPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70" } ], "site_lbl": "Ser265" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86U70-1.245.249", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q86U70-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q86U70-1.267.267", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multiple functions of Ldb1 required for beta-globin activation during erythroid differentiation.", "journal": "Blood", "date": "2010", "authors": "Song SH, Kim A, Ragoczy T, Bender MA, Groudine M, Dean A", "evidence": [ { "database": "iPTMnet", "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70" } ], "reference": [ { "type": "PubMed", "id": "20570862", "url": "https://glygen.org/publication/PubMed/20570862" } ] } ], "crossref": [ { "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20570862", "url": "https://glygen.org/publication/PubMed/20570862", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "M", "down_seq": "VGCACPGCSSKSFKLYSPKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q86U70", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86U70" }, { "database": "PubMed", "id": "20570862", "url": "https://glygen.org/publication/PubMed/20570862" } ], "site_lbl": "Ser2" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86U70-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VAPPAEPTRQQPSKRRKRKM", "down_seq": "GGSTMSSGGGNTNNSNSKKK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "site_lbl": "Ser302" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q86U70-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q86U70-1.318.318", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86U70-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "Q86U70-1", "length": 411, "uniprot_id": "LDB1_HUMAN", "protein_name": "LIM domain-binding protein 1", "refseq_ac": "NP_001106878", "refseq_name": "LIM domain-binding protein 1 isoform 1", "gene_name": "LDB1", "gene_names_uniprotkb": "LDB1; CLIM2", "gene_names_refseq": "CLIM-2; CLIM2; LDB-1; LDB1; NLI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DVGPTPMYPPTYLEPGIGRH", "down_seq": "PYGNQTDYRIFELNKRLQNW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q86U70", "url": "https://www.uniprot.org/uniprotkb/Q86U70" } ], "site_lbl": "Thr61" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "402", "end_pos": "402" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "45", "end_pos": "45" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "245", "end_pos": "249" } ] }, { "type": "snv", "site_list": [ { "start_pos": "263", "end_pos": "263" }, { "start_pos": "267", "end_pos": "267" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "400", "end_pos": "400" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "265", "end_pos": "265" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "61", "end_pos": "61" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q86U70-1.45.45", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs776685221", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776685221", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776685221", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776685221", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748491944", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748491944", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748491944", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748491944", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AQVRVYEPRRDCWLSLPSMP", "down_seq": "PCYGASTFLHGNKIYVLGGR", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr163", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs776685221", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776685221" }, { "id": "rs776685221", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776685221" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "3", "chr_pos": "49174349", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T163", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748491944", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748491944" }, { "id": "rs748491944", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748491944" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "3", "chr_pos": "49174350", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T163", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8IXV7-1.178.178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic analysis of O-GlcNAcylated proteins in invasive ductal breast carcinomas with and without lymph node metastasis.", "journal": "Amino acids", "date": "2016", "authors": "Jiang K, Gao Y, Hou W, Tian F, Ying W, Li L, Bai B, Hou G, Wang PG, Zhang L", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IXV7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IXV7" } ], "reference": [ { "type": "PubMed", "id": "26374642", "url": "https://glygen.org/publication/PubMed/26374642" } ] } ], "crossref": [ { "id": "26374642", "url": "https://glygen.org/publication/PubMed/26374642", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IXV7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IXV7", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "26374642", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26374642" }, { "id": "Q8IXV7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IXV7" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IXV7-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXV7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LPSMPTPCYGASTFLHGNKI", "down_seq": "VLGGRQGKLPVTAFEAFDLE", "snv": [ { "evidence": [ { "id": "Q8IXV7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "3", "chr_pos": "49174395", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y178", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IXV7-1.163.163", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXV7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RHPSLPSRRAFAGCAMAEGS", "down_seq": "FSLGGLQQPGPHNFYSRPHF", "snv": [ { "evidence": [ { "id": "Q8IXV7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "49174870", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V224", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8IXV7-1.239.239", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXV7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MAEGSVFSLGGLQQPGPHNF", "down_seq": "SRPHFVNTVEMFDLEHGSWT", "snv": [ { "evidence": [ { "id": "Q8IXV7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFY->NFS).", "chr_id": "3", "chr_pos": "49174916", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Y239", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IXV7-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IXV7-1.258.258", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IXV7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "FYSRPHFVNTVEMFDLEHGS", "down_seq": "TKLPRSLRMRDKRADFVVGS", "snv": [ { "evidence": [ { "id": "Q8IXV7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IXV7" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "49175069", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "W258", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IXV7-1.239.239", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2045820186", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2045820186", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2045820186", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2045820186#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DFVVGSLGGHIVAIGGLGNQ", "down_seq": "CPLGSVESFSLARRRWEALP", "snv": [ { "evidence": [ { "id": "rs2045820186", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2045820186" }, { "id": "rs2045820186", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2045820186#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQP->NQS).", "chr_id": "3", "chr_pos": "49175613", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P293", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8IXV7-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IXV7-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q8IXV7-1", "length": 354, "uniprot_id": "KLD8B_HUMAN", "protein_name": "Kelch domain-containing protein 8B", "refseq_ac": "NP_775817", "refseq_name": "kelch domain-containing protein 8B", "gene_name": "KLHDC8B", "gene_names_uniprotkb": "KLHDC8B; FP17659", "gene_names_refseq": "CHL; KLHDC8B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IXV7", "url": "https://www.uniprot.org/uniprotkb/Q8IXV7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs148176543", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148176543", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148176543", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148176543", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148176543", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148176543#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148176543", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148176543", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GHIVAIGGLGNQPCPLGSVE", "down_seq": "FSLARRRWEALPAMPTARCS", "snv": [ { "evidence": [ { "id": "rs148176543", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148176543" }, { "id": "rs148176543", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148176543" }, { "id": "rs148176543", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148176543#frequency_tab" }, { "id": "rs148176543", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148176543" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SFS->NFS).", "chr_id": "3", "chr_pos": "49175638", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] }, { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "301", "end_pos": "301" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8IXV7-1.293.293", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the measles virus hemagglutinin bound to the CD46 receptor.", "journal": "Nature structural & molecular biology", "date": "2010-01", "authors": "Santiago C\u00e9sar, Celma Mar\u00eda L, Stehle Thilo, Casasnovas Jos\u00e9 M", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" }, { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "20010840", "url": "https://glygen.org/publication/PubMed/20010840" } ] }, { "title": "Attachment of Neisseria gonorrhoeae to the cellular pilus receptor CD46: identification of domains important for bacterial adherence.", "journal": "Cellular microbiology", "date": "2001", "authors": "Kallstrom H, Blackmer Gill D, Albiger B, Liszewski MK, Atkinson JP, Jonsson AB", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" } ] }, { "title": "The N-glycan of the SCR 2 region is essential for membrane cofactor protein (CD46) to function as a measles virus receptor.", "journal": "Journal of virology", "date": "1996", "authors": "Maisner A, Alvarez J, Liszewski MK, Atkinson DJ, Atkinson JP, Herrler G", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" } ] }, { "title": "Membrane cofactor protein: importance of N- and O-glycosylation for complement regulatory function.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1998", "authors": "Liszewski MK, Leung MK, Atkinson JP", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "crossref": [ { "id": "1CKL", "url": "https://www.rcsb.org/structure/1CKL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1CKL|D|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1CKL|F|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "1CKL|E|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "3L89", "url": "https://www.rcsb.org/structure/3L89", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "20010840", "url": "https://glygen.org/publication/PubMed/20010840", "database": "PubMed", "categories": [ "Other" ] }, { "id": "3INB", "url": "https://www.rcsb.org/structure/3INB", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "3INB|D|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3INB|C|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3L89|V|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3L89|S|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3L89|P|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "3L89|M|80", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CYRETCPYIRDPLNGQAVPA", "down_seq": "GTYEFGYQMHFICNEGYYLI", "glycosylation": [ { "glytoucan_ac": "G22768VO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1CKL&bu=0&command=select+.D:80;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn114", "evidence": [ { "id": "1CKL", "database": "PDB", "url": "https://www.rcsb.org/structure/1CKL" } ] }, { "glytoucan_ac": "G61846BY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1CKL&bu=0&command=select+.E:80;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn114", "evidence": [ { "id": "1CKL", "database": "PDB", "url": "https://www.rcsb.org/structure/1CKL" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=3INB&bu=0&command=select+.D:80;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn114", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" }, { "id": "3L89", "database": "PDB", "url": "https://www.rcsb.org/sequence/3L89" }, { "id": "20010840", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/20010840" }, { "id": "3INB", "database": "PDB", "url": "https://www.rcsb.org/sequence/3INB" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "Q", "comment": "Strongly decreases cytoprotective function. Decreases Neisseria binding. Abolishes Measles virus binding.", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" }, { "database": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" }, { "database": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag" ], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs773650155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773650155", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773650155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773650155", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773650155", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773650155", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKGSVAIWSGKPPICEKVLC", "down_seq": "PPPKIKNGKHTFSEVEVFEY", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr163", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs773650155", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773650155" }, { "id": "rs773650155", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773650155" }, { "id": "rs773650155", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773650155" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "1", "chr_pos": "207761261", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T163", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1501", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Attachment of Neisseria gonorrhoeae to the cellular pilus receptor CD46: identification of domains important for bacterial adherence.", "journal": "Cellular microbiology", "date": "2001", "authors": "Kallstrom H, Blackmer Gill D, Albiger B, Liszewski MK, Atkinson JP, Jonsson AB", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" } ] }, { "title": "The N-glycan of the SCR 2 region is essential for membrane cofactor protein (CD46) to function as a measles virus receptor.", "journal": "Journal of virology", "date": "1996", "authors": "Maisner A, Alvarez J, Liszewski MK, Atkinson DJ, Atkinson JP, Herrler G", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" } ] }, { "title": "Membrane cofactor protein: importance of N- and O-glycosylation for complement regulatory function.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1998", "authors": "Liszewski MK, Leung MK, Atkinson JP", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1501", "url": "https://glyconnect.expasy.org/browser/proteins/1501", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MFECDKGFYLDGSDTIVCDS", "down_seq": "STWDPPVPKCLKVLPPSSTK", "glycosylation": [ { "glytoucan_ac": "G00912UN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G25451PN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G34989PA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G40834TG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G59324HL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSNSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G60033FS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G60177UT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G83229XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G84452RH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G85282JO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86182NS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92406TI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G94470IW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G98611JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GFYLDGSDTIVCDSnSTWDPPVPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn273", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "Q", "comment": "Strongly decreases cytoprotective function. Abolishes Neisseria binding. No effect on Measles virus binding.", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" }, { "database": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" }, { "database": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag" ], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P15529-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 32 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 31 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 31 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 31 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 31 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 31 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CDSNSTWDPPVPKCLKVLPP", "down_seq": "STKPPALSHSVSTSSTTKSP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser290", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSNSTWDPPVPKCLKVLPPS", "down_seq": "TKPPALSHSVSTSSTTKSPA", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser291", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SNSTWDPPVPKCLKVLPPSS", "down_seq": "KPPALSHSVSTSSTTKSPAS", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr292", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2102598940", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102598940", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPVPKCLKVLPPSSTKPPAL", "down_seq": "HSVSTSSTTKSPASSASGPR", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser298", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "1", "chr_pos": "207767642", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S298", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2102598940", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102598940" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->R).", "chr_id": "1", "chr_pos": "207767642", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S298", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VPKCLKVLPPSSTKPPALSH", "down_seq": "VSTSSTTKSPASSASGPRPT", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser300", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.302.302", "start_pos": 302, "end_pos": 302, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KCLKVLPPSSTKPPALSHSV", "down_seq": "TSSTTKSPASSASGPRPTYK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser302", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CLKVLPPSSTKPPALSHSVS", "down_seq": "SSTTKSPASSASGPRPTYKP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr303", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKVLPPSSTKPPALSHSVST", "down_seq": "STTKSPASSASGPRPTYKPP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser304", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVLPPSSTKPPALSHSVSTS", "down_seq": "TTKSPASSASGPRPTYKPPV", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser305", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2526541973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2526541973", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLPPSSTKPPALSHSVSTSS", "down_seq": "TKSPASSASGPRPTYKPPVS", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr306", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2526541973", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2526541973" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "1", "chr_pos": "207767793", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T306", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LPPSSTKPPALSHSVSTSST", "down_seq": "KSPASSASGPRPTYKPPVSN", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr307", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs111519405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs111519405", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs111519405", "url": "https://www.ensembl.org/id/rs111519405", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs111519405", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs111519405", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSSTKPPALSHSVSTSSTTK", "down_seq": "PASSASGPRPTYKPPVSNYP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser309", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs111519405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs111519405" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "1", "chr_pos": "207767803", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S309", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs111519405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs111519405" }, { "id": "rs111519405", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs111519405" }, { "id": "rs111519405", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs111519405" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "NC_000001.11", "chr_pos": "207767803", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S309", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKPPALSHSVSTSSTTKSPA", "down_seq": "SASGPRPTYKPPVSNYPGYP", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser312", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPPALSHSVSTSSTTKSPAS", "down_seq": "ASGPRPTYKPPVSNYPGYPK", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser313", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PALSHSVSTSSTTKSPASSA", "down_seq": "GPRPTYKPPVSNYPGYPKPE", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser315", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P15529-1.298.298", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SVSTSSTTKSPASSASGPRP", "down_seq": "YKPPVSNYPGYPKPEEGILD", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (GalNAc...) threonine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr320", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15529-1.300.300", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] } ], "crossref": [ { "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTKSPASSASGPRPTYKPPV", "down_seq": "NYPGYPKPEEGILDSLDVWV", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser326", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-GalNAcylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "S", "relation": "attached", "comment": "O-linked (GalNAc...) serine;O-GalNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser326", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P15529-1.321.321", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1501", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] }, { "title": "Attachment of Neisseria gonorrhoeae to the cellular pilus receptor CD46: identification of domains important for bacterial adherence.", "journal": "Cellular microbiology", "date": "2001", "authors": "Kallstrom H, Blackmer Gill D, Albiger B, Liszewski MK, Atkinson JP, Jonsson AB", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" } ] }, { "title": "The N-glycan of the SCR 2 region is essential for membrane cofactor protein (CD46) to function as a measles virus receptor.", "journal": "Journal of virology", "date": "1996", "authors": "Maisner A, Alvarez J, Liszewski MK, Atkinson DJ, Atkinson JP, Herrler G", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" } ] }, { "title": "Membrane cofactor protein: importance of N- and O-glycosylation for complement regulatory function.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "1998", "authors": "Liszewski MK, Leung MK, Atkinson JP", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "reference": [ { "type": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1501", "url": "https://glyconnect.expasy.org/browser/proteins/1501", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "1CKL", "url": "https://www.rcsb.org/structure/1CKL", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "1CKL|F|49", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KCKKGYFYIPPLATHTICDR", "down_seq": "HTWLPVSDDACYRETCPYIR", "glycosylation": [ { "glytoucan_ac": "G00912UN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G03644CB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04854VP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G07810QS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G12341GU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G13131HA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G15169WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G19918RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G20706XG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28622IK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G34989PA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43669FQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G50856PC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G61256FT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G69521XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G76417NN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1501", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1501" } ] }, { "glytoucan_ac": "G78649WQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G82443XX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G85282JO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G89827JR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92551JA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G94106MV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=1CKL&bu=0&command=select+.F:49;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "1CKL", "database": "PDB", "url": "https://www.rcsb.org/structure/1CKL" } ] }, { "glytoucan_ac": "G94470IW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYFYIPPLATHTICDRnHTWLPVSDDACYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn83", "evidence": [ { "id": "P15529", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P15529#ptm_processing" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "Q", "comment": "No effect on cytoprotective function. No effect on Neisseria binding. No effect on Measles virus binding.", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "PubMed", "id": "11260136", "url": "https://glygen.org/publication/PubMed/11260136" }, { "database": "PubMed", "id": "8764003", "url": "https://glygen.org/publication/PubMed/8764003" }, { "database": "PubMed", "id": "9759896", "url": "https://glygen.org/publication/PubMed/9759896" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag" ], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P15529-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P15529-1.85.85", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 44 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 43 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 43 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 43 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 43 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 43 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Synthesis of a Highly Azide-Reactive and Thermosensitive Biofunctional Reagent for Efficient Enrichment and Large-Scale Identification of O-GlcNAc Proteins by Mass Spectrometry.", "journal": "Analytical chemistry", "date": "2017", "authors": "Zhang W, Liu T, Dong H, Bai H, Tian F, Shi Z, Chen M, Wang J, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" }, { "database": "O-GlcNAc Atlas", "id": "P15529", "url": "https://oglcnac.org/atlas/detail/P15529" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] } ], "crossref": [ { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P15529", "url": "https://oglcnac.org/atlas/detail/P15529", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKGYFYIPPLATHTICDRNH", "down_seq": "WLPVSDDACYRETCPYIRDP", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr85", "evidence": [ { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "P15529", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P15529" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "P15529", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P15529" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P15529-1.83.83", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NHTWLPVSDDACYRETCPYI", "down_seq": "DPLNGQAVPANGTYEFGYQM", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "207757560", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R103", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P15529-1.83.83", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P15529-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P15529-1.85.85", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P15529-1.114.114", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P15529-1.116.116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1378950364", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1378950364", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1378950364", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1378950364#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RETCPYIRDPLNGQAVPANG", "down_seq": "YEFGYQMHFICNEGYYLIGE", "snv": [ { "evidence": [ { "id": "rs1378950364", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1378950364" }, { "id": "rs1378950364", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1378950364#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->NGA).", "chr_id": "1", "chr_pos": "207757599", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.114.114", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P15529-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AVPANGTYEFGYQMHFICNE", "down_seq": "YYLIGEEILYCELKGSVAIW", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEG->NEC).", "chr_id": "1", "chr_pos": "207757641", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G130", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P15529-1.114.114", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.116.116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MEPPGRRECPFPSW", "down_seq": "FPGLLLAAMVLLLYSFSDAC", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "207752255", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R15", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P15529-1.33.33", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs143544996", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143544996", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143544996", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143544996#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GKKFYYKATVMFECDKGFYL", "down_seq": "GSDTIVCDSNSTWDPPVPKC", "snv": [ { "evidence": [ { "id": "rs143544996", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143544996" }, { "id": "rs143544996", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143544996#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "1", "chr_pos": "207767126", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P15529-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1376898809", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376898809", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1376898809", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376898809", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KFYYKATVMFECDKGFYLDG", "down_seq": "DTIVCDSNSTWDPPVPKCLK", "snv": [ { "evidence": [ { "id": "rs1376898809", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376898809" }, { "id": "rs1376898809", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376898809" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SDT->NDT).", "chr_id": "1", "chr_pos": "207767133", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S265", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P15529-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs747869014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747869014", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747869014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747869014", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747869014", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747869014", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VMFECDKGFYLDGSDTIVCD", "down_seq": "NSTWDPPVPKCLKVLPPSST", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" }, { "id": "rs747869014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747869014" }, { "id": "rs747869014", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747869014" }, { "id": "rs747869014", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747869014" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SNS->NNS).", "chr_id": "1", "chr_pos": "207767154", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S272", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P15529-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P15529-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P15529-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ECDKGFYLDGSDTIVCDSNS", "down_seq": "WDPPVPKCLKVLPPSSTKPP", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->NSN).", "chr_id": "1", "chr_pos": "207767163", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T275", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P15529-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P15529-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P15529-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P15529-1.273.273", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P15529-1.290.290", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P15529-1.291.291", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P15529-1.292.292", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SWRFPGLLLAAMVLLLYSFS", "down_seq": "ACEEPPTFEAMELIGKPKPY", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DAC->NAC).", "chr_id": "1", "chr_pos": "207752309", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D33", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P15529-1.15.15", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "WVIAVIVIAIVVGVAVICVV", "down_seq": "YRYLQRRKKKGTYLTDETHR", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "207785649", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P365", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P15529-1.368.368", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1047780483", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047780483", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1047780483", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1047780483#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1047780483", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047780483", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CKKGYFYIPPLATHTICDRN", "down_seq": "TWLPVSDDACYRETCPYIRD", "snv": [ { "evidence": [ { "id": "rs1047780483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047780483" }, { "id": "rs1047780483", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1047780483#frequency_tab" }, { "id": "rs1047780483", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047780483" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHT->NPT).", "chr_id": "1", "chr_pos": "207757167", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H84", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P15529-1.83.83", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P15529-1.85.85", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P15529-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P15529", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PLATHTICDRNHTWLPVSDD", "down_seq": "CYRETCPYIRDPLNGQAVPA", "snv": [ { "evidence": [ { "id": "P15529", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P15529" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "207757193", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A93", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P15529-1.83.83", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.85.85", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P15529-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P15529-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Membrane cofactor protein (MCP; CD46): isoform-specific tyrosine phosphorylation.", "journal": "Journal of immunology (Baltimore, Md. : 1950)", "date": "2000", "authors": "Wang G, Liszewski MK, Chan AC, Atkinson JP", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "iPTMnet", "id": "P15529", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529" } ], "reference": [ { "type": "PubMed", "id": "10657632", "url": "https://glygen.org/publication/PubMed/10657632" } ] } ], "crossref": [ { "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P15529", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10657632", "url": "https://glygen.org/publication/PubMed/10657632", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VSTSSTTKSPASSASGPRPT", "down_seq": "KPPVSNYPGYPKPEEGILDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "iPTMnet", "id": "P15529", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529" }, { "database": "PubMed", "id": "10657632", "url": "https://glygen.org/publication/PubMed/10657632" } ], "site_lbl": "Tyr321" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P15529-1.302.302", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P15529-1.303.303", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P15529-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P15529-1.305.305", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P15529-1.306.306", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P15529-1.307.307", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P15529-1.309.309", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P15529-1.312.312", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P15529-1.313.313", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P15529-1.315.315", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P15529-1.320.320", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P15529-1.326.326", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P15529-1.368.368", "start_pos": 368, "end_pos": 368, "uniprot_canonical_ac": "P15529-1", "length": 392, "uniprot_id": "MCP_HUMAN", "protein_name": "Membrane cofactor protein", "refseq_ac": "NP_002380", "refseq_name": "membrane cofactor protein isoform 1 precursor", "gene_name": "CD46", "gene_names_uniprotkb": "CD46; MCP; MIC10", "gene_names_refseq": "AHUS2; CD46; MCP; MIC10; TLX; TRA2.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "CD46 is phosphorylated at tyrosine 354 upon infection of epithelial cells by Neisseria gonorrhoeae.", "journal": "J. Cell Biol.", "date": "2002", "authors": "Lee SW, Bonnah RA, Higashi DL, Atkinson JP, Milgram SL, So M", "evidence": [ { "database": "UniProtKB", "id": "P15529", "url": "https://www.uniprot.org/uniprotkb/P15529" }, { "database": "iPTMnet", "id": "P15529-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529-1" } ], "reference": [ { "type": "PubMed", "id": "11901164", "url": "https://glygen.org/publication/PubMed/11901164" } ] } ], "crossref": [ { "id": "P15529", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11901164", "url": "https://glygen.org/publication/PubMed/11901164", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AVIVIAIVVGVAVICVVPYR", "down_seq": "LQRRKKKGTYLTDETHREVK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07947-1", "kinase_gene_name": "YES1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P15529", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P15529" }, { "database": "PubMed", "id": "11901164", "url": "https://glygen.org/publication/PubMed/11901164" } ], "site_lbl": "Tyr368" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "85", "end_pos": "85" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "83", "end_pos": "83" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "93", "end_pos": "93" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "321", "end_pos": "321" }, { "start_pos": "368", "end_pos": "368" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P15529-1.365.365", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER.", "journal": "Molecular cell", "date": "2009", "authors": "Ernst R, Mueller B, Ploegh HL, Schlieker C", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "Reactome", "id": "R-HSA-5689896", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689896" }, { "database": "RefSeq", "id": "NP_001263249", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001263249" } ], "reference": [ { "type": "PubMed", "id": "19818707", "url": "https://glygen.org/publication/PubMed/19818707" } ] }, { "title": "VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy.", "journal": "The EMBO journal", "date": "2017", "authors": "Papadopoulos C, Kirchner P, Bug M, Grum D, Koerver L, Schulze N, Poehler R, Dressler A, Fengler S, Arhzaouy K, Lux V, Ehrmann M, Weihl CC, Meyer H", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "reference": [ { "type": "PubMed", "id": "27753622", "url": "https://glygen.org/publication/PubMed/27753622" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19818707", "url": "https://glygen.org/publication/PubMed/19818707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27753622", "url": "https://glygen.org/publication/PubMed/27753622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "SYVRETLPVLTRTVVPADNS", "down_seq": "LFTSVYYVVEGGVLNPACAP", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "S", "comment": "Abolishes deubiquitinase activity without affecting interaction with VCP. Specifically blocks a step in the course of dislocation and/or degradation of endoplasmic reticulum-resident proteins destined for proteasomal degradation. Prevents the macroautophagy of damaged lysosome membranes decorated with K48-linked ubiquitin chains.", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "PubMed", "id": "19818707", "url": "https://glygen.org/publication/PubMed/19818707" }, { "database": "PubMed", "id": "27753622", "url": "https://glygen.org/publication/PubMed/27753622" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q5VVQ6-1.150.150", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.", "journal": "Cell", "date": "2013", "authors": "Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "Reactome", "id": "R-HSA-5689896", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689896" } ], "reference": [ { "type": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QRNFPDPDTPPLTIFSSNDD", "down_seq": "VLVQALELADEARRRRQFTD", "mutagenesis": [ { "sequence_org": "I", "sequence_mut": "Q", "comment": "Does not affect activity or specificity. Impairs ability to cleave longer 'Lys-11'-linked ubiquitin chains; when associated with Q-295.", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q5VVQ6-1.295.295", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.", "journal": "Cell", "date": "2013", "authors": "Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "Reactome", "id": "R-HSA-5689896", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689896" } ], "reference": [ { "type": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "FPDPDTPPLTIFSSNDDIVL", "down_seq": "QALELADEARRRRQFTDVNR", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "Q", "comment": "Does not affect activity or specificity. Impairs ability to cleave longer 'Lys-11'-linked ubiquitin chains; when associated with Q-292.", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q5VVQ6-1.292.292", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.", "journal": "Cell", "date": "2013", "authors": "Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "Reactome", "id": "R-HSA-5689896", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689896" } ], "reference": [ { "type": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "FTLRCMVCQKGLTGQAEARE", "down_seq": "AKETGHTNFGEV", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Reduced activity toward 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked ubiquitin without affecting activity toward 'Lys-11'-linked ubiquitin; when associated with A-342.", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q5VVQ6-1.342.342", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "OTU deubiquitinases reveal mechanisms of linkage specificity and enable ubiquitin chain restriction analysis.", "journal": "Cell", "date": "2013", "authors": "Mevissen TE, Hospenthal MK, Geurink PP, Elliott PR, Akutsu M, Arnaudo N, Ekkebus R, Kulathu Y, Wauer T, El Oualid F, Freund SM, Ovaa H, Komander D", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "Reactome", "id": "R-HSA-5689896", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689896" } ], "reference": [ { "type": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "VCQKGLTGQAEAREHAKETG", "down_seq": "TNFGEV", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Reduced activity toward 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked ubiquitin without affecting activity toward 'Lys-11'-linked ubiquitin; when associated with A-336.", "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" }, { "database": "PubMed", "id": "23827681", "url": "https://glygen.org/publication/PubMed/23827681" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q5VVQ6-1.336.336", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VVQ6-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "Q5VVQ6-1", "length": 348, "uniprot_id": "OTU1_HUMAN", "protein_name": "Ubiquitin thioesterase OTU1", "refseq_ac": "NP_001263249", "refseq_name": "ubiquitin thioesterase OTU1 isoform 2", "gene_name": "YOD1", "gene_names_uniprotkb": "YOD1; DUBA8; HIN7; OTUD2; PRO0907", "gene_names_refseq": "DUBA-8; DUBA8; HIN-7; OTUD2; PRO0907; YOD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VVQ6", "url": "https://www.uniprot.org/uniprotkb/Q5VVQ6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q5VVQ6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VVQ6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q5VVQ6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VVQ6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPAFTKRGASSYVRETLPVL", "down_seq": "RTVVPADNSCLFTSVYYVVE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q5VVQ6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VVQ6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr150" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "342", "end_pos": "342" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "150", "end_pos": "150" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q5VVQ6-1.160.160", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs766296817", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766296817", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766296817", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766296817", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs766296817", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs766296817", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MESRDHNNPQEGP", "down_seq": "SSSGRRAAVEDNHLLIKAVQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr14", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs766296817", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817" }, { "id": "rs766296817", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817" }, { "id": "rs766296817", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766296817" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->K).", "chr_id": "1", "chr_pos": "182586766", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T14", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" }, { "id": "rs766296817", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817" }, { "id": "rs766296817", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766296817" }, { "id": "rs766296817", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766296817" }, { "id": "rs766296817", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs766296817" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "1", "chr_pos": "182586766", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T14", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05823-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05823-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.607.607", "start_pos": 607, "end_pos": 607, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q05823", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05823" }, { "database": "O-GlcNAc Atlas", "id": "Q05823", "url": "https://oglcnac.org/atlas/detail/Q05823" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05823", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05823", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q05823", "url": "https://oglcnac.org/atlas/detail/Q05823", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs773548267", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773548267", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773548267", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773548267", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773548267", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773548267", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "WTWESRYRTLRNVGNESDIK", "down_seq": "RKSESEILRLLQPGPSEHSK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr607", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q05823", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05823" }, { "id": "Q05823", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q05823" } ] } ], "snv": [ { "evidence": [ { "id": "rs773548267", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773548267" }, { "id": "rs773548267", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773548267" }, { "id": "rs773548267", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773548267" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "1", "chr_pos": "182581310", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T607", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q05823-1.595.595", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05823-1.597.597", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action.", "journal": "Cell", "date": "1993", "authors": "Zhou A, Hassel BA, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AITHLLLDHGADVNVRGERG", "down_seq": "TPLILAVEKKHLGLVQRLLE", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "N", "comment": "Reduced 2-5A binding activity; almost complete loss of 2-5A binding activity; when associated with N-274.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05823-1.235.235", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action.", "journal": "Cell", "date": "1993", "authors": "Zhou A, Hassel BA, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LVQRLLEQEHIEINDTDSDG", "down_seq": "TALLLAVELKLKKIAELLCK", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "N", "comment": "Reduced 2-5A binding activity; almost complete loss of 2-5A binding activity; when associated with N-240.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "7680958", "url": "https://glygen.org/publication/PubMed/7680958" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Alternative function of a protein kinase homology domain in 2', 5'-oligoadenylate dependent RNase L.", "journal": "Nucleic acids research", "date": "1999", "authors": "Dong B, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "9862963", "url": "https://glygen.org/publication/PubMed/9862963" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9862963", "url": "https://glygen.org/publication/PubMed/9862963", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ADTSEGGIYLGFYEKQEVAV", "down_seq": "TFCEGSPRAQREVSCLQSSR", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "R", "comment": "Complete loss of enzymatic activity and enzyme dimerization. No change in binding to 2-5A and RNA.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "9862963", "url": "https://glygen.org/publication/PubMed/9862963" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q05823-1.373.373", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.583.583", "start_pos": 583, "end_pos": 583, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IHRLFHPGEHVRDCLSDLLG", "down_seq": "PFFWTWESRYRTLRNVGNES", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "No change in enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q05823-1.584.584", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05823-1.595.595", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05823-1.597.597", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.584.584", "start_pos": 584, "end_pos": 584, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HRLFHPGEHVRDCLSDLLGH", "down_seq": "FFWTWESRYRTLRNVGNESD", "mutagenesis": [ { "sequence_org": "P", "sequence_mut": "A", "comment": "No change in enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q05823-1.583.583", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05823-1.595.595", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q05823-1.597.597", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "SEILRLLQPGPSEHSKSFDK", "down_seq": "TTKINECVMKKMNKFYEKRG", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "No change in enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q05823-1.631.631", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05823-1.646.646", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.661.661", "start_pos": 661, "end_pos": 661, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MKKMNKFYEKRGNFYQNTVG", "down_seq": "LLKFIRNLGEHIDEEKHKKM", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Complete loss of enzymatic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q05823-1.646.646", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q05823-1.667.667", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05823-1.672.672", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.667.667", "start_pos": 667, "end_pos": 667, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FYEKRGNFYQNTVGDLLKFI", "down_seq": "NLGEHIDEEKHKKMKLKIGD", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Complete loss of enzymatic activity. No change in 2-5A binding and enzyme dimerization.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q05823-1.661.661", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05823-1.672.672", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.672.672", "start_pos": 672, "end_pos": 672, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Basis for regulated RNA cleavage by functional analysis of RNase L and Ire1p.", "journal": "RNA (New York, N.Y.)", "date": "2001", "authors": "Dong B, Niwa M, Walter P, Silverman RH", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "reference": [ { "type": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "crossref": [ { "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GNFYQNTVGDLLKFIRNLGE", "down_seq": "IDEEKHKKMKLKIGDPSLYF", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Complete loss of enzymatic activity. No change in 2-5A binding activity and enzyme dimerization.", "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" }, { "database": "PubMed", "id": "11333017", "url": "https://glygen.org/publication/PubMed/11333017" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q05823-1.661.661", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q05823-1.667.667", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05823-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RKTKEDQERLRKGGATALMD", "down_seq": "AEKGHVEVLKILLDEMGADV", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "182586284", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A175", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769537958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769537958", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769537958", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769537958#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769537958", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769537958", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EVLKILLDEMGADVNACDNM", "down_seq": "RNALIHALLSSDDSDVEAIT", "snv": [ { "evidence": [ { "id": "rs769537958", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958" }, { "id": "rs769537958", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958" }, { "id": "rs769537958", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769537958#frequency_tab" }, { "id": "rs769537958", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769537958" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMG->NMC).", "chr_id": "1", "chr_pos": "182586203", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G202", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769537958", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958" }, { "id": "rs769537958", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769537958" }, { "id": "rs769537958", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769537958#frequency_tab" }, { "id": "rs769537958", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769537958" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMG->NMS).", "chr_id": "1", "chr_pos": "182586203", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G202", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.235.235", "start_pos": 235, "end_pos": 235, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1661590503", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661590503", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1661590503", "url": "https://www.ensembl.org/id/rs1661590503", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DSDVEAITHLLLDHGADVNV", "down_seq": "GERGKTPLILAVEKKHLGLV", "snv": [ { "evidence": [ { "id": "rs1661590503", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661590503" }, { "id": "rs1661590503", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1661590503" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVR->NVS).", "chr_id": "1", "chr_pos": "182586102", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R235", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q05823-1.240.240", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2102372712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102372712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102372712", "url": "https://www.ensembl.org/id/rs2102372712", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NPQEGPTSSSGRRAAVEDNH", "down_seq": "LIKAVQNEDVDLVQQLLEGG", "snv": [ { "evidence": [ { "id": "rs2102372712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102372712" }, { "id": "rs2102372712", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102372712" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHL->NHS).", "chr_id": "1", "chr_pos": "182586724", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L28", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q05823-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q05823-1.14.14", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.310.310", "start_pos": 310, "end_pos": 310, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELLCKRGASTDCGDLVMTAR", "down_seq": "NYDHSLVKVLLSHGAKEDFH", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "182585879", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R310", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1336299614", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336299614", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1336299614", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336299614", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IYRPMIGKLKFFIDEKYKIA", "down_seq": "TSEGGIYLGFYEKQEVAVKT", "snv": [ { "evidence": [ { "id": "rs1336299614", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336299614" }, { "id": "rs1336299614", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336299614" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTS->NTS).", "chr_id": "1", "chr_pos": "182585690", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D373", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q05823-1.392.392", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SHLVTFYGSESHRGHLFVCV", "down_seq": "LCEQTLEACLDVHRGEDVEN", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TLC->NLC).", "chr_id": "1", "chr_pos": "182585503", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T435", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EACLDVHRGEDVENEEDEFA", "down_seq": "NVLSSIFKAVQELHLSCGYT", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "182585422", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R462", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2102372450", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102372450", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102372450", "url": "https://www.ensembl.org/id/rs2102372450", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AVQNEDVDLVQQLLEGGANV", "down_seq": "FQEEEGGWTPLHNAVQMSRE", "snv": [ { "evidence": [ { "id": "rs2102372450", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102372450" }, { "id": "rs2102372450", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102372450" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVN->NVT).", "chr_id": "1", "chr_pos": "182586652", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N52", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371715795", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371715795", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371715795", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371715795", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371715795", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371715795#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371715795", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371715795", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVKRDLEDLGRLVLYVVKKG", "down_seq": "ISFEDLKAQSNEEVVQLSPD", "snv": [ { "evidence": [ { "id": "rs371715795", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371715795" }, { "id": "rs371715795", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371715795" }, { "id": "rs371715795", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371715795#frequency_tab" }, { "id": "rs371715795", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371715795" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SIS->NIS).", "chr_id": "1", "chr_pos": "182582218", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S536", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.595.595", "start_pos": 595, "end_pos": 595, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DCLSDLLGHPFFWTWESRYR", "down_seq": "LRNVGNESDIKTRKSESEIL", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "182581346", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T595", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q05823-1.583.583", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05823-1.584.584", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q05823-1.597.597", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05823-1.607.607", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.597.597", "start_pos": 597, "end_pos": 597, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSDLLGHPFFWTWESRYRTL", "down_seq": "NVGNESDIKTRKSESEILRL", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "182581341", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R597", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q05823-1.583.583", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q05823-1.584.584", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q05823-1.595.595", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05823-1.607.607", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.631.631", "start_pos": 631, "end_pos": 631, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1178962643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1178962643", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1178962643", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1178962643", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ESEILRLLQPGPSEHSKSFD", "down_seq": "WTTKINECVMKKMNKFYEKR", "snv": [ { "evidence": [ { "id": "rs1178962643", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1178962643" }, { "id": "rs1178962643", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1178962643" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KWT->NWT).", "chr_id": "1", "chr_pos": "182581237", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K631", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q05823-1.632.632", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q05823-1.646.646", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.646.646", "start_pos": 646, "end_pos": 646, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SKSFDKWTTKINECVMKKMN", "down_seq": "FYEKRGNFYQNTVGDLLKFI", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "182576358", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K646", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q05823-1.631.631", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q05823-1.632.632", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q05823-1.661.661", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1429102716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1429102716", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1429102716", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1429102716", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DIVELLLRHGADPVLRKKNG", "down_seq": "TPFILAAIAGSVKLLKLFLS", "snv": [ { "evidence": [ { "id": "rs1429102716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1429102716" }, { "id": "rs1429102716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1429102716" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "1", "chr_pos": "182586530", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A93", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1429102716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1429102716" }, { "id": "rs1429102716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1429102716" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "1", "chr_pos": "182586530", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A93", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q05823-1.99.99", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05823", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LRHGADPVLRKKNGATPFIL", "down_seq": "AIAGSVKLLKLFLSKGADVN", "snv": [ { "evidence": [ { "id": "Q05823", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05823" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "182586512", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A99", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q05823-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05823-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "Q05823-1", "length": 741, "uniprot_id": "RN5A_HUMAN", "protein_name": "2-5A-dependent ribonuclease", "refseq_ac": "NP_066956", "refseq_name": "2-5A-dependent ribonuclease", "gene_name": "RNASEL", "gene_names_uniprotkb": "RNASEL; RNS4", "gene_names_refseq": "PRCA1; RNASEL; RNS4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05823", "url": "https://www.uniprot.org/uniprotkb/Q05823" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1376540253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376540253", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1376540253", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1376540253#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1376540253", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376540253", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MESRDHNN", "down_seq": "QEGPTSSSGRRAAVEDNHLL", "snv": [ { "evidence": [ { "id": "rs1376540253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376540253" }, { "id": "rs1376540253", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1376540253#frequency_tab" }, { "id": "rs1376540253", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376540253" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNS).", "chr_id": "1", "chr_pos": "182586782", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P9", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1376540253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376540253" }, { "id": "rs1376540253", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1376540253#frequency_tab" }, { "id": "rs1376540253", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376540253" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNT).", "chr_id": "1", "chr_pos": "182586782", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P9", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "607", "end_pos": "607" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "240", "end_pos": "240" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "672", "end_pos": "672" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "595", "end_pos": "595" }, { "start_pos": "597", "end_pos": "597" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "646", "end_pos": "646" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q05823-1.14.14", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q05823-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P0C7M6-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P0C7M6-1", "length": 154, "uniprot_id": "IQCF3_HUMAN", "protein_name": "IQ domain-containing protein F3", "refseq_ac": "NP_001078948", "refseq_name": "IQ domain-containing protein F3", "gene_name": "IQCF3", "gene_names_uniprotkb": "IQCF3", "gene_names_refseq": "IQCF3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0C7M6", "url": "https://www.uniprot.org/uniprotkb/P0C7M6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P0C7M6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "", "down_seq": "QKLLLAQLHHRKRVKAAGQI", "snv": [ { "evidence": [ { "id": "P0C7M6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51829704", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R20", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P0C7M6-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P0C7M6-1", "length": 154, "uniprot_id": "IQCF3_HUMAN", "protein_name": "IQ domain-containing protein F3", "refseq_ac": "NP_001078948", "refseq_name": "IQ domain-containing protein F3", "gene_name": "IQCF3", "gene_names_uniprotkb": "IQCF3", "gene_names_refseq": "IQCF3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0C7M6", "url": "https://www.uniprot.org/uniprotkb/P0C7M6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P0C7M6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LAQLHHRKRVKAAGQIQAWW", "down_seq": "GVLVRRTLLVAALRAWMIQC", "snv": [ { "evidence": [ { "id": "P0C7M6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51830470", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R45", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "P0C7M6-1.50.50", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P0C7M6-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P0C7M6-1", "length": 154, "uniprot_id": "IQCF3_HUMAN", "protein_name": "IQ domain-containing protein F3", "refseq_ac": "NP_001078948", "refseq_name": "IQ domain-containing protein F3", "gene_name": "IQCF3", "gene_names_uniprotkb": "IQCF3", "gene_names_refseq": "IQCF3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0C7M6", "url": "https://www.uniprot.org/uniprotkb/P0C7M6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P0C7M6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HRKRVKAAGQIQAWWRGVLV", "down_seq": "RTLLVAALRAWMIQCWWRTL", "snv": [ { "evidence": [ { "id": "P0C7M6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "5", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51830484", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R50", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P0C7M6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "51830485", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R50", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P0C7M6-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P0C7M6-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P0C7M6-1", "length": 154, "uniprot_id": "IQCF3_HUMAN", "protein_name": "IQ domain-containing protein F3", "refseq_ac": "NP_001078948", "refseq_name": "IQ domain-containing protein F3", "gene_name": "IQCF3", "gene_names_uniprotkb": "IQCF3", "gene_names_refseq": "IQCF3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P0C7M6", "url": "https://www.uniprot.org/uniprotkb/P0C7M6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P0C7M6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QRRIRQRRQALLRVYVIQEQ", "down_seq": "TVKLQSCIRMWQCRQCYRQM", "snv": [ { "evidence": [ { "id": "P0C7M6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P0C7M6" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "51830611", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A92", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14657-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q14657-1", "length": 143, "uniprot_id": "LAGE3_HUMAN", "protein_name": "EKC/KEOPS complex subunit LAGE3", "refseq_ac": "NP_006005", "refseq_name": "EKC/KEOPS complex subunit LAGE3", "gene_name": "LAGE3", "gene_names_uniprotkb": "LAGE3; DXS9879E; ESO3; ITBA2", "gene_names_refseq": "CVG5; DXS9879E; DXS9951E; ESO3; GAMOS2; ITBA2; LAGE3; Pcc1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14657", "url": "https://www.uniprot.org/uniprotkb/Q14657" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14657", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14657", "url": "https://oglcnac.org/atlas/detail/Q14657", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs2069247966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2069247966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2069247966", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2069247966#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NFLDQLSLVVRTMQRFGPPV", "down_seq": "", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser142", "evidence": [ { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "Q14657", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14657" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q14657", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q14657" } ] }, { "glytoucan_ac": "G70994MS", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser142", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "GLY_000142", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000142" } ] } ], "snv": [ { "evidence": [ { "id": "rs2069247966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2069247966" }, { "id": "rs2069247966", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2069247966#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "X", "chr_pos": "154477951", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S142", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14657-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "Q14657-1", "length": 143, "uniprot_id": "LAGE3_HUMAN", "protein_name": "EKC/KEOPS complex subunit LAGE3", "refseq_ac": "NP_006005", "refseq_name": "EKC/KEOPS complex subunit LAGE3", "gene_name": "LAGE3", "gene_names_uniprotkb": "LAGE3; DXS9879E; ESO3; ITBA2", "gene_names_refseq": "CVG5; DXS9879E; DXS9951E; ESO3; GAMOS2; ITBA2; LAGE3; Pcc1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14657", "url": "https://www.uniprot.org/uniprotkb/Q14657" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1557211336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557211336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1557211336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1557211336", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q14657", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14657", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1212327415", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212327415", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1212327415", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1212327415#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1212327415", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212327415", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SAARGSRMRPHIFTLSVPFP", "down_seq": "PLEAEIAHGSLAPDAEPHQR", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr71", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1557211336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1557211336" }, { "id": "rs1557211336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1557211336" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "X", "chr_pos": "154478389", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T71", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q14657", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14657" }, { "id": "rs1212327415", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1212327415" }, { "id": "rs1212327415", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1212327415#frequency_tab" }, { "id": "rs1212327415", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1212327415" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "23", "chr_pos": "154478388", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T71", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q14657-1.79.79", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14657-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "Q14657-1", "length": 143, "uniprot_id": "LAGE3_HUMAN", "protein_name": "EKC/KEOPS complex subunit LAGE3", "refseq_ac": "NP_006005", "refseq_name": "EKC/KEOPS complex subunit LAGE3", "gene_name": "LAGE3", "gene_names_uniprotkb": "LAGE3; DXS9879E; ESO3; ITBA2", "gene_names_refseq": "CVG5; DXS9879E; DXS9951E; ESO3; GAMOS2; ITBA2; LAGE3; Pcc1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14657", "url": "https://www.uniprot.org/uniprotkb/Q14657" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14657", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14657", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RPHIFTLSVPFPTPLEAEIA", "down_seq": "GSLAPDAEPHQRVVGKDLTV", "snv": [ { "evidence": [ { "id": "Q14657", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14657" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "154478365", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H79", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14657-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1648783653", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1648783653", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1648783653", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1648783653#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1648783653", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1648783653", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RVIQVWFQNCRARHKKHVSP", "down_seq": "HSSSTPVTAVPPSRLSPPML", "glycosylation": [ { "glytoucan_ac": "G57883XA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HVSPNHSSSTPVTAVPPSR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn287", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] } ], "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" }, { "id": "rs1648783653", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1648783653" }, { "id": "rs1648783653", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1648783653#frequency_tab" }, { "id": "rs1648783653", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1648783653" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NHS->KHS).", "chr_id": "1", "chr_pos": "75156943", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N287", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NHS->SHS).", "chr_id": "1", "chr_pos": "75156942", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N287", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q68G74-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q68G74-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68G74-1.289.289", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68G74-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs914929165", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs914929165", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs914929165", "url": "https://www.ensembl.org/id/rs914929165", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VDKYLLKVNDLCWHVRCLSC", "down_seq": "VCRTSLGRHTSCYIKDKDIF", "snv": [ { "evidence": [ { "id": "rs914929165", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs914929165" }, { "id": "rs914929165", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs914929165" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SVC->NVC).", "chr_id": "1", "chr_pos": "75141025", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S103", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q68G74-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2100337826", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100337826", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2100337826", "url": "https://www.ensembl.org/id/rs2100337826", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DLCWHVRCLSCSVCRTSLGR", "down_seq": "TSCYIKDKDIFCKLDYFRRY", "snv": [ { "evidence": [ { "id": "rs2100337826", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100337826" }, { "id": "rs2100337826", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2100337826" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HTS->NTS).", "chr_id": "1", "chr_pos": "75141051", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H112", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68G74-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2523265369", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2523265369", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SRCGRHIHSTDWVRRAKGNV", "down_seq": "HLACFACFSCKRQLSTGEEF", "snv": [ { "evidence": [ { "id": "rs2523265369", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2523265369" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVY->NVC).", "chr_id": "1", "chr_pos": "75143198", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y157", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1255473604", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255473604", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1255473604", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1255473604#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1255473604", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255473604", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LCRVHYDCMLDNLKREVENG", "down_seq": "GISVEGALLTEQDVNHPKPA", "snv": [ { "evidence": [ { "id": "rs1255473604", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255473604" }, { "id": "rs1255473604", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1255473604#frequency_tab" }, { "id": "rs1255473604", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255473604" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGN->NGS).", "chr_id": "1", "chr_pos": "75143848", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N205", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KLAERTGLSRRVIQVWFQNC", "down_seq": "ARHKKHVSPNHSSSTPVTAV", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NCR->NCT).", "chr_id": "1", "chr_pos": "75156912", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R277", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q68G74-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q68G74-1.287.287", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68G74-1.289.289", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AERTGLSRRVIQVWFQNCRA", "down_seq": "HKKHVSPNHSSSTPVTAVPP", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "1", "chr_pos": "75156917", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R279", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q68G74-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q68G74-1.287.287", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q68G74-1.289.289", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1465664677", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465664677", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1465664677", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1465664677#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1465664677", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465664677", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IQVWFQNCRARHKKHVSPNH", "down_seq": "SSTPVTAVPPSRLSPPMLEE", "snv": [ { "evidence": [ { "id": "rs1465664677", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1465664677" }, { "id": "rs1465664677", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1465664677#frequency_tab" }, { "id": "rs1465664677", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1465664677" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHS->NHP).", "chr_id": "1", "chr_pos": "75156947", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S289", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68G74-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q68G74-1.279.279", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68G74-1.287.287", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PSRLSPPMLEEMAYSAYVPQ", "down_seq": "GTMLTALHSYMDAHSPTTLG", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DGT->NGT).", "chr_id": "1", "chr_pos": "75157037", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D319", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TALAAGRTRKGAGEEGLVSP", "down_seq": "GAGDEDSCSSSAPLSPSSSP", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "75137109", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E39", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q68G74-1.55.55", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LVSPEGAGDEDSCSSSAPLS", "down_seq": "SSSPRSMASGSGCPPGKCVC", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "75137158", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P55", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68G74-1.39.39", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68G74-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q68G74-1", "length": 356, "uniprot_id": "LHX8_HUMAN", "protein_name": "LIM/homeobox protein Lhx8", "refseq_ac": "NP_001001933", "refseq_name": "LIM/homeobox protein Lhx8 isoform 1", "gene_name": "LHX8", "gene_names_uniprotkb": "LHX8", "gene_names_refseq": "LHX7; LHX8", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68G74", "url": "https://www.uniprot.org/uniprotkb/Q68G74" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68G74", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MQIL", "down_seq": "RCQGLMSEECGRTTALAAGR", "snv": [ { "evidence": [ { "id": "Q68G74", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68G74" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SRC->NRC).", "chr_id": "1", "chr_pos": "75130728", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S5", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "287", "end_pos": "287" } ] }, { "type": "snv", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "5", "end_pos": "5" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9NPA3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9NPA3-1", "length": 183, "uniprot_id": "M1IP1_HUMAN", "protein_name": "Mid1-interacting protein 1", "refseq_ac": "NP_001092260", "refseq_name": "mid1-interacting protein 1", "gene_name": "MID1IP1", "gene_names_uniprotkb": "MID1IP1; MIG12", "gene_names_refseq": "G12-like; MID1IP1; MIG12; S14R; STRAIT11499; THRSPL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Synthesis of a Highly Azide-Reactive and Thermosensitive Biofunctional Reagent for Efficient Enrichment and Large-Scale Identification of O-GlcNAc Proteins by Mass Spectrometry.", "journal": "Analytical chemistry", "date": "2017", "authors": "Zhang W, Liu T, Dong H, Bai H, Tian F, Shi Z, Chen M, Wang J, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9NPA3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NPA3" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NPA3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NPA3", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q9NPA3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NPA3" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "75", "end_pos": "75" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NPA3-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q9NPA3-1", "length": 183, "uniprot_id": "M1IP1_HUMAN", "protein_name": "Mid1-interacting protein 1", "refseq_ac": "NP_001092260", "refseq_name": "mid1-interacting protein 1", "gene_name": "MID1IP1", "gene_names_uniprotkb": "MID1IP1; MIG12", "gene_names_refseq": "G12-like; MID1IP1; MIG12; S14R; STRAIT11499; THRSPL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" }, { "database": "iPTMnet", "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVGGSGGCLEERTPPVPDSG", "down_seq": "ANGSFFAPSRDMYSHYVLLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3" } ], "site_lbl": "Ser75" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "75", "end_pos": "75" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q9NPA3-1.79.79", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NPA3-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "Q9NPA3-1", "length": 183, "uniprot_id": "M1IP1_HUMAN", "protein_name": "Mid1-interacting protein 1", "refseq_ac": "NP_001092260", "refseq_name": "mid1-interacting protein 1", "gene_name": "MID1IP1", "gene_names_uniprotkb": "MID1IP1; MIG12", "gene_names_refseq": "G12-like; MID1IP1; MIG12; S14R; STRAIT11499; THRSPL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" }, { "database": "iPTMnet", "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGGCLEERTPPVPDSGSANG", "down_seq": "FFAPSRDMYSHYVLLKSIRN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9NPA3", "url": "https://www.uniprot.org/uniprotkb/Q9NPA3" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9NPA3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NPA3" } ], "site_lbl": "Ser79" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "75", "end_pos": "75" }, { "start_pos": "79", "end_pos": "79" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q9NPA3-1.75.75", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75427", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427" }, { "database": "O-GlcNAc Atlas", "id": "O75427", "url": "https://oglcnac.org/atlas/detail/O75427" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "O75427", "url": "https://oglcnac.org/atlas/detail/O75427", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NLSNRRLKHFPRGAARSYDL", "down_seq": "DITQADLSRNRFPEVPEAAC", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser68", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75427", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427" }, { "id": "O75427", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75427" } ] } ], "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "7", "chr_pos": "100585898", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S68", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O75427-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75427-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75427-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75427-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75427", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427" }, { "database": "O-GlcNAc Atlas", "id": "O75427", "url": "https://oglcnac.org/atlas/detail/O75427" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "O75427", "url": "https://oglcnac.org/atlas/detail/O75427", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1462969296", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1462969296", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1462969296", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1462969296", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200251319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200251319", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200251319", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200251319", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200251319", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200251319", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200251319", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200251319#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200251319", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200251319", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NRRLKHFPRGAARSYDLSDI", "down_seq": "QADLSRNRFPEVPEAACQLV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr71", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75427", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75427" }, { "id": "O75427", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75427" } ] } ], "snv": [ { "evidence": [ { "id": "rs1462969296", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1462969296" }, { "id": "rs1462969296", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1462969296" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "7", "chr_pos": "100585890", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T71", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200251319", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200251319" }, { "id": "rs200251319", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200251319" }, { "id": "rs200251319", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200251319" }, { "id": "rs200251319", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200251319#frequency_tab" }, { "id": "rs200251319", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200251319" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "7", "chr_pos": "100585889", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T71", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75427-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75427-1.68.68", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75427-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75427-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1801440122", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1801440122", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1801440122", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1801440122#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1801440122", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1801440122", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NPLQSPPAQVCLKGKLHIFK", "down_seq": "LSTEAGQRGSALGDLAPSRP", "snv": [ { "evidence": [ { "id": "rs1801440122", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1801440122" }, { "id": "rs1801440122", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1801440122#frequency_tab" }, { "id": "rs1801440122", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1801440122" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YLS->NLS).", "chr_id": "7", "chr_pos": "100578478", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y257", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "APSRPPSFSPCPAEDLFPGH", "down_seq": "YDGGLDSGFHSVDSGSKRWS", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "100578230", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R293", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75427-1.279.279", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O75427-1.281.281", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O75427-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75427-1.307.307", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75427-1.309.309", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75427-1.313.313", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GGLDSGFHSVDSGSKRWSGN", "down_seq": "STDEFSELSFRISELAREPR", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "E", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "7", "chr_pos": "100578160", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E316", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75427-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75427-1.307.307", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75427-1.309.309", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75427-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75427-1.336.336", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ESTDEFSELSFRISELAREP", "down_seq": "GPRERKEDGSADGDPVQIDF", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "7", "chr_pos": "100577855", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R336", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75427-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs139180317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139180317", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139180317", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139180317", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139180317", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139180317", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GSPGLPGRRSAERALEEAVA", "down_seq": "GTLNLSNRRLKHFPRGAARS", "snv": [ { "evidence": [ { "id": "rs139180317", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139180317" }, { "id": "rs139180317", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139180317" }, { "id": "rs139180317", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139180317" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TGT->NGT).", "chr_id": "7", "chr_pos": "100585970", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75427-1.25.25", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75427-1.53.53", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.461.461", "start_pos": 461, "end_pos": 461, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369601562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369601562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369601562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369601562", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369601562", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369601562#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369601562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369601562", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VVGGAAAVSTQAMHNGSPKS", "down_seq": "ASQAGAAAGQGAPAPAPASQ", "snv": [ { "evidence": [ { "id": "rs369601562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369601562" }, { "id": "rs369601562", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369601562" }, { "id": "rs369601562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369601562#frequency_tab" }, { "id": "rs369601562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369601562" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAS->NAS).", "chr_id": "7", "chr_pos": "100576988", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S461", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O75427-1.457.457", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748420896", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748420896", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748420896", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748420896#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748420896", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748420896", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SAERALEEAVATGTLNLSNR", "down_seq": "LKHFPRGAARSYDLSDITQA", "snv": [ { "evidence": [ { "id": "rs748420896", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896" }, { "id": "rs748420896", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896" }, { "id": "rs748420896", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748420896#frequency_tab" }, { "id": "rs748420896", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748420896" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRC).", "chr_id": "7", "chr_pos": "100585944", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R53", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748420896", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896" }, { "id": "rs748420896", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748420896" }, { "id": "rs748420896", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748420896#frequency_tab" }, { "id": "rs748420896", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748420896" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRS).", "chr_id": "7", "chr_pos": "100585944", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R53", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O75427-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75427-1.68.68", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75427-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75427-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.545.545", "start_pos": 545, "end_pos": 545, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VLRPRRYPQVPDEKDLMTQL", "down_seq": "QVLESRLQRPLPEDLAEALA", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "100576242", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R545", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LSNRRLKHFPRGAARSYDLS", "down_seq": "ITQADLSRNRFPEVPEAACQ", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DIT->NIT).", "chr_id": "7", "chr_pos": "100585896", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D69", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75427-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75427-1.68.68", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75427-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75427-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1318893369", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318893369", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1318893369", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1318893369", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LKHFPRGAARSYDLSDITQA", "down_seq": "LSRNRFPEVPEAACQLVSLE", "snv": [ { "evidence": [ { "id": "O75427", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75427" }, { "id": "rs1318893369", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318893369" }, { "id": "rs1318893369", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1318893369" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "7", "chr_pos": "100585881", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D74", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O75427-1.68.68", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75427-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75427-1.71.71", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RQLDVSSNELQSLPSELCGL", "down_seq": "SLRDLNVRRNQLSTLPEELG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser182" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O75427-1.183.183", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLDVSSNELQSLPSELCGLS", "down_seq": "LRDLNVRRNQLSTLPEELGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Ser183" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O75427-1.182.182", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Exploring the human leukocyte phosphoproteome using a microfluidic reversed-phase-TiO2-reversed-phase high-performance liquid chromatography phosphochip coupled to a quadrupole time-of-flight mass spectrometer.", "journal": "Analytical chemistry", "date": "2010", "authors": "Raijmakers R, Kraiczek K, de Jong AP, Mohammed S, Heck AJ", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VAAPLAAGGEEAAATTSVPG", "down_seq": "PGLPGRRSAERALEEAVATG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser25" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "O75427-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.279.279", "start_pos": 279, "end_pos": 279, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STEAGQRGSALGDLAPSRPP", "down_seq": "FSPCPAEDLFPGHRYDGGLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "site_lbl": "Ser279" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75427-1.281.281", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAGQRGSALGDLAPSRPPSF", "down_seq": "PCPAEDLFPGHRYDGGLDSG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "site_lbl": "Ser281" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75427-1.279.279", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAEDLFPGHRYDGGLDSGFH", "down_seq": "VDSGSKRWSGNESTDEFSEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser304" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75427-1.307.307", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75427-1.309.309", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75427-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75427-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DLFPGHRYDGGLDSGFHSVD", "down_seq": "GSKRWSGNESTDEFSELSFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser307" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75427-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75427-1.309.309", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75427-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75427-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FPGHRYDGGLDSGFHSVDSG", "down_seq": "KRWSGNESTDEFSELSFRIS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser309" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75427-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75427-1.307.307", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75427-1.313.313", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75427-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RYDGGLDSGFHSVDSGSKRW", "down_seq": "GNESTDEFSELSFRISELAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "site_lbl": "Ser313" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75427-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75427-1.304.304", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75427-1.307.307", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75427-1.309.309", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75427-1.316.316", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75427-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QERERRQQQQSGAWGAPRKD", "down_seq": "LLKPGLRAVVGGAAAVSTQA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser432" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLRAVVGGAAAVSTQAMHNG", "down_seq": "PKSSASQAGAAAGQGAPAPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser457" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "O75427-1.461.461", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.511.511", "start_pos": 511, "end_pos": 511, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAPAPRPLGSIQRPNSFLFR", "down_seq": "SSQSGSGPSSPDSVLRPRRY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser511" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75427-1.513.513", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75427-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75427-1.517.517", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75427-1.521.521", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.513.513", "start_pos": 513, "end_pos": 513, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAPRPLGSIQRPNSFLFRSS", "down_seq": "QSGSGPSSPDSVLRPRRYPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser513" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75427-1.511.511", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75427-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75427-1.517.517", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75427-1.521.521", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.515.515", "start_pos": 515, "end_pos": 515, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRPLGSIQRPNSFLFRSSSQ", "down_seq": "GSGPSSPDSVLRPRRYPQVP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser515" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O75427-1.511.511", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75427-1.513.513", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75427-1.517.517", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75427-1.521.521", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLGSIQRPNSFLFRSSSQSG", "down_seq": "GPSSPDSVLRPRRYPQVPDE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser517" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "O75427-1.511.511", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75427-1.513.513", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75427-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75427-1.521.521", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.521.521", "start_pos": 521, "end_pos": 521, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IQRPNSFLFRSSSQSGSGPS", "down_seq": "PDSVLRPRRYPQVPDEKDLM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser521" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O75427-1.511.511", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O75427-1.513.513", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75427-1.515.515", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75427-1.517.517", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75427-1.589.589", "start_pos": 589, "end_pos": 589, "uniprot_canonical_ac": "O75427-1", "length": 683, "uniprot_id": "LRCH4_HUMAN", "protein_name": "Leucine-rich repeat and calponin homology domain-containing protein 4", "refseq_ac": "NP_001276863", "refseq_name": "leucine-rich repeat and calponin homology domain-containing protein 4 isoform 2", "gene_name": "LRCH4", "gene_names_uniprotkb": "LRCH4; LRN; LRRN1; LRRN4", "gene_names_refseq": "LRCH4; LRN; LRRN1; LRRN4; PP14183", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ILCQLANQLRPRSVPFIHVP", "down_seq": "PAVPKLSALKARKNVESFLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75427", "url": "https://www.uniprot.org/uniprotkb/O75427" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75427", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75427" } ], "site_lbl": "Ser589" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "68", "end_pos": "68" }, { "start_pos": "71", "end_pos": "71" } ] }, { "type": "snv", "site_list": [ { "start_pos": "257", "end_pos": "257" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "545", "end_pos": "545" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "74", "end_pos": "74" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "182", "end_pos": "182" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "279", "end_pos": "279" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "589", "end_pos": "589" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9UJL9-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "Q9UJL9-1", "length": 534, "uniprot_id": "ZF69B_HUMAN", "protein_name": "Zinc finger protein 69 homolog B", "refseq_ac": "NP_075558", "refseq_name": "zinc finger protein 69 homolog B", "gene_name": "ZFP69B", "gene_names_uniprotkb": "ZFP69B; ZNF643", "gene_names_refseq": "ZFP69B; ZKSCAN23B; ZNF643; ZSCAN54B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9UJL9", "url": "https://www.uniprot.org/uniprotkb/Q9UJL9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9UJL9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UJL9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSSDLKSKTKTKESALQNDI", "down_seq": "WEELHCGLMMERFTKGSSMY", "snv": [ { "evidence": [ { "id": "Q9UJL9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9UJL9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "40462472", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S163", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "163", "end_pos": "163" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2I0M4-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q2I0M4-1", "length": 334, "uniprot_id": "LRC26_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 26", "refseq_ac": "NP_001013675", "refseq_name": "leucine-rich repeat-containing protein 26 precursor", "gene_name": "LRRC26", "gene_names_uniprotkb": "LRRC26; CAPC", "gene_names_refseq": "CAPC; LRRC26; bA350O14.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1452", "url": "https://glyconnect.expasy.org/browser/proteins/1452" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "BK potassium channel modulation by leucine-rich repeat-containing proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2012", "authors": "Yan J, Aldrich RW", "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4#ptm_processing" }, { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "reference": [ { "type": "PubMed", "id": "22547800", "url": "https://glygen.org/publication/PubMed/22547800" } ] } ], "crossref": [ { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1452", "url": "https://glyconnect.expasy.org/browser/proteins/1452", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22547800", "url": "https://glygen.org/publication/PubMed/22547800", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8VAV", "url": "https://www.rcsb.org/structure/8VAV", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "8VAV|E|147", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VAV|F|147", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VAV|H|147", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "8VAV|G|147", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SANQLEALAPGTFAPLRALR", "down_seq": "LSLAGNRLARLEPAALGALP", "glycosylation": [ { "glytoucan_ac": "G64527OM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn147", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1452", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1452" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=8VAV&bu=0&command=select+.E:147;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn147", "evidence": [ { "id": "Q2I0M4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4#ptm_processing" }, { "id": "22547800", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22547800" }, { "id": "8VAV", "database": "PDB", "url": "https://www.rcsb.org/structure/8VAV" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "147", "end_pos": "147" } ] }, { "type": "snv", "site_list": [ { "start_pos": "149", "end_pos": "149" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "288", "end_pos": "288" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "228", "end_pos": "228" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q2I0M4-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "icn3d_view.label", "icn3d_view.url" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q2I0M4-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "Q2I0M4-1", "length": 334, "uniprot_id": "LRC26_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 26", "refseq_ac": "NP_001013675", "refseq_name": "leucine-rich repeat-containing protein 26 precursor", "gene_name": "LRRC26", "gene_names_uniprotkb": "LRRC26; CAPC", "gene_names_refseq": "CAPC; LRRC26; bA350O14.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1425017990", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1425017990", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1425017990", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1425017990", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NQLEALAPGTFAPLRALRNL", "down_seq": "LAGNRLARLEPAALGALPLL", "snv": [ { "evidence": [ { "id": "rs1425017990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1425017990" }, { "id": "rs1425017990", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1425017990" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NL*).", "chr_id": "9", "chr_pos": "137169498", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S149", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "147", "end_pos": "147" } ] }, { "type": "snv", "site_list": [ { "start_pos": "149", "end_pos": "149" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "288", "end_pos": "288" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "228", "end_pos": "228" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q2I0M4-1.147.147", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2I0M4-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "Q2I0M4-1", "length": 334, "uniprot_id": "LRC26_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 26", "refseq_ac": "NP_001013675", "refseq_name": "leucine-rich repeat-containing protein 26 precursor", "gene_name": "LRRC26", "gene_names_uniprotkb": "LRRC26; CAPC", "gene_names_refseq": "CAPC; LRRC26; bA350O14.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q2I0M4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2I0M4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SRPRPLLLLLLLLSPWPVWA", "down_seq": "VSATASPSGSLGAPDCPEVC", "snv": [ { "evidence": [ { "id": "Q2I0M4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q2I0M4" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "3", "frequency": "3.3", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (3.3%).", "chr_id": "9", "chr_pos": "137169863", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q27", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "147", "end_pos": "147" } ] }, { "type": "snv", "site_list": [ { "start_pos": "149", "end_pos": "149" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "288", "end_pos": "288" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "228", "end_pos": "228" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2I0M4-1.288.288", "start_pos": 288, "end_pos": 288, "uniprot_canonical_ac": "Q2I0M4-1", "length": 334, "uniprot_id": "LRC26_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 26", "refseq_ac": "NP_001013675", "refseq_name": "leucine-rich repeat-containing protein 26 precursor", "gene_name": "LRRC26", "gene_names_uniprotkb": "LRRC26; CAPC", "gene_names_refseq": "CAPC; LRRC26; bA350O14.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1238745578", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238745578", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1238745578", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238745578", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LGPASFLVSLASCLALGSGL", "down_seq": "ACRARRRRLRTAALRPPRPP", "snv": [ { "evidence": [ { "id": "rs1238745578", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238745578" }, { "id": "rs1238745578", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1238745578" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TAC->NAC).", "chr_id": "9", "chr_pos": "137168996", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T288", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "147", "end_pos": "147" } ] }, { "type": "snv", "site_list": [ { "start_pos": "149", "end_pos": "149" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "288", "end_pos": "288" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "228", "end_pos": "228" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q2I0M4-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "Q2I0M4-1", "length": 334, "uniprot_id": "LRC26_HUMAN", "protein_name": "Leucine-rich repeat-containing protein 26", "refseq_ac": "NP_001013675", "refseq_name": "leucine-rich repeat-containing protein 26 precursor", "gene_name": "LRRC26", "gene_names_uniprotkb": "LRRC26; CAPC", "gene_names_refseq": "CAPC; LRRC26; bA350O14.10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q2I0M4", "url": "https://www.uniprot.org/uniprotkb/Q2I0M4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.", "journal": "Molecular immunology", "date": "2020-07", "authors": "Pandey Kirti, Mifsud Nicole A, Lim Kam Sian Terry C C, Ayala Rochelle, Ternette Nicola, Ramarathinam Sri H, Purcell Anthony W", "evidence": [ { "database": "iPTMnet", "id": "Q2I0M4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q2I0M4" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q2I0M4", "url": "https://www.iedb.org/epitope/Q2I0M4", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q2I0M4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q2I0M4", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ALRPLCAWLRRHPLPASEAE", "down_seq": "VLCVWPGRLTLSPLTAFSDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q2I0M4", "url": "https://www.iedb.org/epitope/Q2I0M4" }, { "database": "iPTMnet", "id": "Q2I0M4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q2I0M4" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Thr228" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "147", "end_pos": "147" } ] }, { "type": "snv", "site_list": [ { "start_pos": "149", "end_pos": "149" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "288", "end_pos": "288" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "228", "end_pos": "228" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Synthesis of a Highly Azide-Reactive and Thermosensitive Biofunctional Reagent for Efficient Enrichment and Large-Scale Identification of O-GlcNAc Proteins by Mass Spectrometry.", "journal": "Analytical chemistry", "date": "2017", "authors": "Zhang W, Liu T, Dong H, Bai H, Tian F, Shi Z, Chen M, Wang J, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q13637", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13637" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q13637", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13637" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13637", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13637", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q13637", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13637" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rab32 is an A-kinase anchoring protein and participates in mitochondrial dynamics.", "journal": "The Journal of cell biology", "date": "2002", "authors": "Alto NM, Soderling J, Scott JD", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "RefSeq", "id": "NP_006825", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_006825" } ], "reference": [ { "type": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HGFAGWFETSAKDNINIEEA", "down_seq": "RFLVEKILVNHQSFPNEEND", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "F", "comment": "Abolishes binding to protein kinase A type II regulatory subunit.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q13637-1.188.188", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rab32 is an A-kinase anchoring protein and participates in mitochondrial dynamics.", "journal": "The Journal of cell biology", "date": "2002", "authors": "Alto NM, Soderling J, Scott JD", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "RefSeq", "id": "NP_006825", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_006825" } ], "reference": [ { "type": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AGWFETSAKDNINIEEAARF", "down_seq": "VEKILVNHQSFPNEENDVDK", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "P", "comment": "Abolishes binding to protein kinase A type II regulatory subunit.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q13637-1.185.185", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Rab32 is an A-kinase anchoring protein and participates in mitochondrial dynamics.", "journal": "The Journal of cell biology", "date": "2002", "authors": "Alto NM, Soderling J, Scott JD", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "RefSeq", "id": "NP_006825", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_006825" } ], "reference": [ { "type": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PETREHLFKVLVIGELGVGK", "down_seq": "SIIKRYVHQLFSQHYRATIG", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "N", "comment": "Decreased GTP-binding activity.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "12186851", "url": "https://glygen.org/publication/PubMed/12186851" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular cloning, bacterial expression and properties of Rab31 and Rab32.", "journal": "European journal of biochemistry", "date": "2002", "authors": "Bao X, Faris AE, Jang EK, Haslam RJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "Reactome", "id": "R-HSA-8876198", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8876198" } ], "reference": [ { "type": "PubMed", "id": "11784320", "url": "https://glygen.org/publication/PubMed/11784320" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11784320", "url": "https://glygen.org/publication/PubMed/11784320", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "KVLNWDSRTLVRLQLWDIAG", "down_seq": "ERFGNMTRVYYKEAVGAFVV", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "L", "comment": "No change in GTPase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "11784320", "url": "https://glygen.org/publication/PubMed/11784320" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13637-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13637-1.93.93", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13637-1.94.94", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.", "journal": "Developmental cell", "date": "2014", "authors": "Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "reference": [ { "type": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WDSRTLVRLQLWDIAGQERF", "down_seq": "NMTRVYYKEAVGAFVVFDIS", "mutagenesis": [ { "sequence_org": "G", "sequence_mut": "T", "comment": "Impairs interaction with ANKRD27; when associated with S-90 and L-94.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13637-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13637-1.93.93", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13637-1.94.94", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.", "journal": "Developmental cell", "date": "2014", "authors": "Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "reference": [ { "type": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DSRTLVRLQLWDIAGQERFG", "down_seq": "MTRVYYKEAVGAFVVFDISR", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "S", "comment": "Impairs interaction with ANKRD27; when associated with T-89 and L-94.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13637-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13637-1.93.93", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13637-1.94.94", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.", "journal": "Developmental cell", "date": "2014", "authors": "Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "reference": [ { "type": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "SRTLVRLQLWDIAGQERFGN", "down_seq": "TRVYYKEAVGAFVVFDISRS", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "S", "comment": "Impairs interaction with ANKRD27; when associated with S-93.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q13637-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13637-1.93.93", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13637-1.94.94", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.", "journal": "Developmental cell", "date": "2014", "authors": "Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "reference": [ { "type": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TLVRLQLWDIAGQERFGNMT", "down_seq": "VYYKEAVGAFVVFDISRSST", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "S", "comment": "Impairs interaction with ANKRD27; when associated with M-91.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13637-1.94.94", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "VARP is recruited on to endosomes by direct interaction with retromer, where together they function in export to the cell surface.", "journal": "Developmental cell", "date": "2014", "authors": "Hesketh GG, Perez-Dorado I, Jackson LP, Wartosch L, Schafer IB, Gray SR, McCoy AJ, Zeldin OB, Garman EF, Harbour ME, Evans PR, Seaman MNJ, Luzio JP, Owen DJ", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "reference": [ { "type": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LVRLQLWDIAGQERFGNMTR", "down_seq": "YYKEAVGAFVVFDISRSSTF", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "L", "comment": "Impairs interaction with ANKRD27; when associated with T-89 and S-90.", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "24856514", "url": "https://glygen.org/publication/PubMed/24856514" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13637-1.93.93", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13637", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13637", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KRYVHQLFSQHYRATIGVDF", "down_seq": "LKVLNWDSRTLVRLQLWDIA", "snv": [ { "evidence": [ { "id": "Q13637", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13637" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "6", "chr_pos": "146544058", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A63", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q13637-1.71.71", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13637-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "TiO(2)-based phosphoproteomic analysis of the plasma membrane and the effects of phosphatase inhibitor treatment.", "journal": "Journal of proteome research", "date": "2008", "authors": "Thingholm TE, Larsen MR, Ingrell CR, Kassem M, Jensen ON", "evidence": [ { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Mol. Cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NGSPIPAVLLANKCDQNKDS", "down_seq": "QSPSQVDQFCKEHGFAGWFE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" }, { "database": "PubMed", "id": "18578522", "url": "https://glygen.org/publication/PubMed/18578522" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser152" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13637-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "Q13637-1", "length": 225, "uniprot_id": "RAB32_HUMAN", "protein_name": "Ras-related protein Rab-32", "refseq_ac": "NP_006825", "refseq_name": "ras-related protein Rab-32", "gene_name": "RAB32", "gene_names_uniprotkb": "RAB32", "gene_names_refseq": "PARK26; RAB32", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.", "journal": "Mol. Cell", "date": "2008", "authors": "Daub H, Olsen JV, Bairlein M, Gnad F, Oppermann FS, Korner R, Greff Z, Keri G, Stemmann O, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SQHYRATIGVDFALKVLNWD", "down_seq": "RTLVRLQLWDIAGQERFGNM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13637", "url": "https://www.uniprot.org/uniprotkb/Q13637" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q13637", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13637" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "snv", "site_list": [ { "start_pos": "63", "end_pos": "63" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "152", "end_pos": "152" }, { "start_pos": "71", "end_pos": "71" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q13637-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13637-1.85.85", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13637-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13637-1.90.90", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q13637-1.91.91", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8N7C3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8N7C3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N7C3" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8N7C3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N7C3", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q8N7C3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8N7C3" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8N7C3-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N7C3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VGRENMEKLKESEARASEQV", "down_seq": "SLLKLIVELEKKCGEGTLAL", "snv": [ { "evidence": [ { "id": "Q8N7C3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "188099103", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R185", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N7C3-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N7C3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "WTLWVFPPLKRLFLEKKLDT", "down_seq": "GVFLDCEHGQISFYNVTEMS", "snv": [ { "evidence": [ { "id": "Q8N7C3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "V", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "188091579", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V370", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N7C3-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N7C3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PTRLFCDVDQITLCSKCFQS", "down_seq": "EHKHHMVCGIQEAAENYRKL", "snv": [ { "evidence": [ { "id": "Q8N7C3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "188105234", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q45", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N7C3-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N7C3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KHHMVCGIQEAAENYRKLFQ", "down_seq": "ILNTSREKLEAAKSILTDEQ", "snv": [ { "evidence": [ { "id": "Q8N7C3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "188104920", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E68", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8N7C3-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q8N7C3-1", "length": 437, "uniprot_id": "TRIMM_HUMAN", "protein_name": "Probable E3 ubiquitin-protein ligase TRIML2", "refseq_ac": "NP_001290348", "refseq_name": "probable E3 ubiquitin-protein ligase TRIML2 isoform 1", "gene_name": "TRIML2", "gene_names_uniprotkb": "TRIML2; SPRYD6", "gene_names_refseq": "SPRYD6; TRIML2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8N7C3", "url": "https://www.uniprot.org/uniprotkb/Q8N7C3" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8N7C3", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TSREKLEAAKSILTDEQERM", "down_seq": "MIQEEEQNFKKMIESEYSMR", "snv": [ { "evidence": [ { "id": "Q8N7C3", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7C3" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "188104847", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A92", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "185", "end_pos": "185" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75608-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O75608-1", "length": 230, "uniprot_id": "LYPA1_HUMAN", "protein_name": "Acyl-protein thioesterase 1", "refseq_ac": "NP_001266289", "refseq_name": "acyl-protein thioesterase 1 isoform 6", "gene_name": "LYPLA1", "gene_names_uniprotkb": "LYPLA1; APT1; LPL1", "gene_names_refseq": "APT-1; APT1; LPL-I; LPL1; LYPLA1; hAPT1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multi-comparative Thermal Proteome Profiling Uncovers New O-GlcNAc Proteins in a System-wide Method.", "journal": "Analytical chemistry", "date": "2022-12-29", "authors": "Wang Guoli, Li Yang, Wang Ting, Wang Jun, Yao Jun, Yan Guoquan, Zhang Ying, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75608", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608" } ], "reference": [ { "type": "PubMed", "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75608", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75608", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "O75608", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "36580660", "url": "https://glygen.org/publication/PubMed/36580660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75608", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "36580660", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36580660" }, { "id": "O75608", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75608" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" } ] }, { "type": "snv", "site_list": [ { "start_pos": "210", "end_pos": "210" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75608-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "O75608-1", "length": 230, "uniprot_id": "LYPA1_HUMAN", "protein_name": "Acyl-protein thioesterase 1", "refseq_ac": "NP_001266289", "refseq_name": "acyl-protein thioesterase 1 isoform 6", "gene_name": "LYPLA1", "gene_names_uniprotkb": "LYPLA1; APT1; LPL1", "gene_names_refseq": "APT-1; APT1; LPL-I; LPL1; LYPLA1; hAPT1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "S-acylation of p62 promotes p62 droplet recruitment into autophagosomes in mammalian autophagy.", "journal": "Molecular cell", "date": "2023-10-05", "authors": "Huang Xue, Yao Jia, Liu Lu, Chen Jing, Mei Ligang, Huangfu Jingjing, Luo Dong, Wang Xinyi, Lin Changhai, Chen Xiaorong, Yang Yi, Ouyang Sheng, Wei Fujing, Wang Zhuolin, Zhang Shaolin, Xiang Tingxiu, Neculai Dante, Sun Qiming, Kong Eryan, Tate Edward W, Yang Aimin", "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "reference": [ { "type": "PubMed", "id": "37802024", "url": "https://glygen.org/publication/PubMed/37802024" } ] }, { "title": "Thioesterase activity and subcellular localization of acylprotein thioesterase 1/lysophospholipase 1.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Hirano T, Kishi M, Sugimoto H, Taguchi R, Obinata H, Ohshima N, Tatei K, Izumi T", "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "reference": [ { "type": "PubMed", "id": "19439193", "url": "https://glygen.org/publication/PubMed/19439193" } ] } ], "crossref": [ { "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "37802024", "url": "https://glygen.org/publication/PubMed/37802024", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19439193", "url": "https://glygen.org/publication/PubMed/19439193", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LIDQEVKNGIPSNRIILGGF", "down_seq": "QGGALSLYTALTTQQKLAGV", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Loss of thioesterase and lysophospholipase activity.", "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" }, { "database": "PubMed", "id": "37802024", "url": "https://glygen.org/publication/PubMed/37802024" }, { "database": "PubMed", "id": "19439193", "url": "https://glygen.org/publication/PubMed/19439193" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" } ] }, { "type": "snv", "site_list": [ { "start_pos": "210", "end_pos": "210" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75608-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "O75608-1", "length": 230, "uniprot_id": "LYPA1_HUMAN", "protein_name": "Acyl-protein thioesterase 1", "refseq_ac": "NP_001266289", "refseq_name": "acyl-protein thioesterase 1 isoform 6", "gene_name": "LYPLA1", "gene_names_uniprotkb": "LYPLA1; APT1; LPL1", "gene_names_refseq": "APT-1; APT1; LPL-I; LPL1; LYPLA1; hAPT1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior.", "journal": "eLife", "date": "2018", "authors": "Sadeghi RS, Kulej K, Kathayat RS, Garcia BA, Dickinson BC, Brady DC, Witze ES", "evidence": [ { "database": "iPTMnet", "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608" } ], "reference": [ { "type": "PubMed", "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538" } ] } ], "crossref": [ { "id": "O75608", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75608", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KTLVNPANVTFKTYEGMMHS", "down_seq": "CQQEMMDVKQFIDKLLPPID", "snv": [ { "evidence": [ { "id": "O75608", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75608" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "54051022", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S210", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608" }, { "database": "PubMed", "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538" } ], "site_lbl": "Ser210" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" } ] }, { "type": "snv", "site_list": [ { "start_pos": "210", "end_pos": "210" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O75608-1.209.209", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75608-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "O75608-1", "length": 230, "uniprot_id": "LYPA1_HUMAN", "protein_name": "Acyl-protein thioesterase 1", "refseq_ac": "NP_001266289", "refseq_name": "acyl-protein thioesterase 1 isoform 6", "gene_name": "LYPLA1", "gene_names_uniprotkb": "LYPLA1; APT1; LPL1", "gene_names_refseq": "APT-1; APT1; LPL-I; LPL1; LYPLA1; hAPT1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75608", "url": "https://www.uniprot.org/uniprotkb/O75608" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior.", "journal": "eLife", "date": "2018", "authors": "Sadeghi RS, Kulej K, Kathayat RS, Garcia BA, Dickinson BC, Brady DC, Witze ES", "evidence": [ { "database": "iPTMnet", "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608" } ], "reference": [ { "type": "PubMed", "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538" } ] } ], "crossref": [ { "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKTLVNPANVTFKTYEGMMH", "down_seq": "SCQQEMMDVKQFIDKLLPPI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75608", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75608" }, { "database": "PubMed", "id": "29648538", "url": "https://glygen.org/publication/PubMed/29648538" } ], "site_lbl": "Ser209" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "119", "end_pos": "119" } ] }, { "type": "snv", "site_list": [ { "start_pos": "210", "end_pos": "210" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "210", "end_pos": "210" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O75608-1.210.210", "categories": [ "snv_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H008-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "Q9H008-1", "length": 270, "uniprot_id": "LHPP_HUMAN", "protein_name": "Phospholysine phosphohistidine inorganic pyrophosphate phosphatase", "refseq_ac": "NP_001305261", "refseq_name": "phospholysine phosphohistidine inorganic pyrophosphate phosphatase isoform 4", "gene_name": "LHPP", "gene_names_uniprotkb": "LHPP", "gene_names_refseq": "HDHD2B; LHPP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H008", "url": "https://www.uniprot.org/uniprotkb/Q9H008" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H008", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VRGVLLDISGVLYDSGAGGG", "down_seq": "AIAGSVEAVARLKRSRLKVR", "snv": [ { "evidence": [ { "id": "Q9H008", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "2", "frequency": "2.2", "sequence_org": "T", "sequence_mut": "K", "comment": "Somatic mutation passed 2 filters: patient freq. (2.2%); num. of cancers (3).", "chr_id": "10", "chr_pos": "124461954", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T31", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "31", "end_pos": "31" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "230", "end_pos": "230" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H008-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q9H008-1", "length": 270, "uniprot_id": "LHPP_HUMAN", "protein_name": "Phospholysine phosphohistidine inorganic pyrophosphate phosphatase", "refseq_ac": "NP_001305261", "refseq_name": "phospholysine phosphohistidine inorganic pyrophosphate phosphatase isoform 4", "gene_name": "LHPP", "gene_names_uniprotkb": "LHPP", "gene_names_refseq": "HDHD2B; LHPP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H008", "url": "https://www.uniprot.org/uniprotkb/Q9H008" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H008", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PSPEFFKSALQAIGVEAHQA", "down_seq": "MIGDDIVGDVGGAQRCGMRA", "snv": [ { "evidence": [ { "id": "Q9H008", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "124517183", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V210", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "31", "end_pos": "31" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "230", "end_pos": "230" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9H008-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9H008-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H008-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "Q9H008-1", "length": 270, "uniprot_id": "LHPP_HUMAN", "protein_name": "Phospholysine phosphohistidine inorganic pyrophosphate phosphatase", "refseq_ac": "NP_001305261", "refseq_name": "phospholysine phosphohistidine inorganic pyrophosphate phosphatase isoform 4", "gene_name": "LHPP", "gene_names_uniprotkb": "LHPP", "gene_names_refseq": "HDHD2B; LHPP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H008", "url": "https://www.uniprot.org/uniprotkb/Q9H008" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H008", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AIGVEAHQAVMIGDDIVGDV", "down_seq": "GAQRCGMRALQVRTGKFRPS", "snv": [ { "evidence": [ { "id": "Q9H008", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "124517216", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G221", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "31", "end_pos": "31" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "230", "end_pos": "230" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H008-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9H008-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H008-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "Q9H008-1", "length": 270, "uniprot_id": "LHPP_HUMAN", "protein_name": "Phospholysine phosphohistidine inorganic pyrophosphate phosphatase", "refseq_ac": "NP_001305261", "refseq_name": "phospholysine phosphohistidine inorganic pyrophosphate phosphatase isoform 4", "gene_name": "LHPP", "gene_names_uniprotkb": "LHPP", "gene_names_refseq": "HDHD2B; LHPP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H008", "url": "https://www.uniprot.org/uniprotkb/Q9H008" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H008", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VMIGDDIVGDVGGAQRCGMR", "down_seq": "LQVRTGKFRPSDEHHPEVKA", "snv": [ { "evidence": [ { "id": "Q9H008", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H008" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "124517244", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A230", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "31", "end_pos": "31" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "230", "end_pos": "230" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9H008-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9H008-1.221.221", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q969X1-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "Q969X1-1", "length": 311, "uniprot_id": "LFG3_HUMAN", "protein_name": "Protein lifeguard 3", "refseq_ac": "NP_001308356", "refseq_name": "protein lifeguard 3 isoform 1", "gene_name": "TMBIM1", "gene_names_uniprotkb": "TMBIM1; LFG3; PP1201; PSEC0158; RECS1", "gene_names_refseq": "LFG3; MST100; MSTP100; PP1201; RECS1; TMBIM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q969X1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q969X1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YGQPSVLPGGYPAYPGYPQP", "down_seq": "YGHPAGYPQPMPPTHPMPMN", "snv": [ { "evidence": [ { "id": "Q969X1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q969X1" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "218282005", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G46", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "46", "end_pos": "46" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q969X1-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q969X1-1", "length": 311, "uniprot_id": "LFG3_HUMAN", "protein_name": "Protein lifeguard 3", "refseq_ac": "NP_001308356", "refseq_name": "protein lifeguard 3 isoform 1", "gene_name": "TMBIM1", "gene_names_uniprotkb": "TMBIM1; LFG3; PP1201; PSEC0158; RECS1", "gene_names_refseq": "LFG3; MST100; MSTP100; PP1201; RECS1; TMBIM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome of resting human platelets.", "journal": "J. Proteome Res.", "date": "2008", "authors": "Zahedi RP, Lewandrowski U, Wiesner J, Wortelkamp S, Moebius J, Schutz C, Walter U, Gambaryan S, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" }, { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" } ], "reference": [ { "type": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HPMPMNYGPGHGYDGEERAV", "down_seq": "DSFGPGEWDDRKVRHTFIRK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" }, { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" }, { "database": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "46", "end_pos": "46" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q969X1-1.83.83", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q969X1-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "Q969X1-1", "length": 311, "uniprot_id": "LFG3_HUMAN", "protein_name": "Protein lifeguard 3", "refseq_ac": "NP_001308356", "refseq_name": "protein lifeguard 3 isoform 1", "gene_name": "TMBIM1", "gene_names_uniprotkb": "TMBIM1; LFG3; PP1201; PSEC0158; RECS1", "gene_names_refseq": "LFG3; MST100; MSTP100; PP1201; RECS1; TMBIM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" }, { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MPMNYGPGHGYDGEERAVSD", "down_seq": "FGPGEWDDRKVRHTFIRKVY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q969X1", "url": "https://www.uniprot.org/uniprotkb/Q969X1" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q969X1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q969X1" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser83" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "46", "end_pos": "46" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" }, { "start_pos": "83", "end_pos": "83" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q969X1-1.81.81", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9HAT1-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SHHGDAILGLEEVRLTPSMR", "down_seq": "RSGAVWSRASVPFSAWEVEV", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn75", "evidence": [ { "id": "Q9HAT1", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.79.79", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs3803568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3803568", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs3803568", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs3803568", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs3803568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3803568", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs3803568", "url": "https://www.ncbi.nlm.nih.gov/snp/rs3803568#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs3803568", "url": "http://gnomad.broadinstitute.org/awesome?query=rs3803568", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs3803568", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs3803568", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2063889823", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063889823", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2063889823", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2063889823", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2063889823", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2063889823", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SVPFSAWEVEVQMRVTGLGR", "down_seq": "GAQGMAVWYTRGRGHVGSVL", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs3803568", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3803568" }, { "id": "rs3803568", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs3803568" }, { "id": "rs3803568", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3803568" }, { "id": "rs3803568", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs3803568#frequency_tab" }, { "id": "rs3803568", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs3803568" }, { "id": "rs3803568", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs3803568" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816295", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R105", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs2063889823", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063889823" }, { "id": "rs2063889823", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2063889823" }, { "id": "rs2063889823", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2063889823" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816294", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R105", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs530685001", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs530685001", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530685001", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs530685001", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs530685001", "url": "https://www.ncbi.nlm.nih.gov/snp/rs530685001#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs530685001", "url": "http://gnomad.broadinstitute.org/awesome?query=rs530685001", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs530685001", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530685001", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1386161428", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386161428", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1386161428", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1386161428#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1386161428", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386161428", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TRGRGHVGSVLGGLASWDGI", "down_seq": "IFFDSPAEDTQDSPAIRVLA", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs530685001", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001" }, { "id": "rs530685001", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530685001" }, { "id": "rs530685001", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001" }, { "id": "rs530685001", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs530685001#frequency_tab" }, { "id": "rs530685001", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs530685001" }, { "id": "rs530685001", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530685001" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816499", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G135", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1386161428", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386161428" }, { "id": "rs1386161428", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1386161428#frequency_tab" }, { "id": "rs1386161428", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386161428" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816500", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G135", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1386161428", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1386161428" }, { "id": "rs1386161428", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1386161428#frequency_tab" }, { "id": "rs1386161428", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1386161428" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816500", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G135", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs530685001", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001" }, { "id": "rs530685001", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530685001" }, { "id": "rs530685001", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530685001" }, { "id": "rs530685001", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs530685001#frequency_tab" }, { "id": "rs530685001", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs530685001" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816499", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G135", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.143.143", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.147.147", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.150.150", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.155.155", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1567224801", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567224801", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567224801", "url": "https://www.ensembl.org/id/rs1567224801", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1567224805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567224805", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567224805", "url": "https://www.ensembl.org/id/rs1567224805", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LRLARQLEGLWARLGLGTRE", "down_seq": "VTPKSDSEAQGEGERLFDLE", "snv": [ { "evidence": [ { "id": "rs1567224801", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567224801" }, { "id": "rs1567224801", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567224801" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (DVT->NVT); glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74820728", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D290", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1567224805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567224805" }, { "id": "rs1567224805", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567224805" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74820729", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.287.287", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.296.296", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.308.308", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.310.310", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.377.377", "start_pos": 377, "end_pos": 377, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1337093915", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337093915", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1337093915", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337093915#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1337093915", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337093915", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ASCQIPSTPGRGGHLSMSLN", "down_seq": "DSAKVGALLHGQWTLLQALQ", "snv": [ { "evidence": [ { "id": "rs1337093915", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337093915" }, { "id": "rs1337093915", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337093915#frequency_tab" }, { "id": "rs1337093915", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337093915" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (KDS->NDS); glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74821900", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K377", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.364.364", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.365.365", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.370.370", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.383.383", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.390.390", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.397.397", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.490.490", "start_pos": 490, "end_pos": 490, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2063937466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063937466", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2063937466", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063937466#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2063937466", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2063937466", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs909490238", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs909490238", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs909490238", "url": "https://www.ncbi.nlm.nih.gov/snp/rs909490238#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs909490238", "url": "http://gnomad.broadinstitute.org/awesome?query=rs909490238", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLIQTVGFFGYVHFRQELNK", "down_seq": "LQECLSTGSLPLGPAPHTPR", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs2063937466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063937466" }, { "id": "rs2063937466", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063937466#frequency_tab" }, { "id": "rs2063937466", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2063937466" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74825493", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S490", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs909490238", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs909490238" }, { "id": "rs909490238", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs909490238#frequency_tab" }, { "id": "rs909490238", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs909490238" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74825494", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S490", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.470.470", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.472.472", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.473.473", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.476.476", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.477.477", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.480.480", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.481.481", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.482.482", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.486.486", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.489.489", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.491.491", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.492.492", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.493.493", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.494.494", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.496.496", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.498.498", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.500.500", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.503.503", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.504.504", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.506.506", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.507.507", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.510.510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1471656721", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471656721", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1471656721", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471656721#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1471656721", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471656721", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1471656721", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1471656721", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VWSRASVPFSAWEVEVQMRV", "down_seq": "GLGRRGAQGMAVWYTRGRGH", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs1471656721", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471656721" }, { "id": "rs1471656721", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471656721#frequency_tab" }, { "id": "rs1471656721", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471656721" }, { "id": "rs1471656721", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1471656721" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816280", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T100", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762709699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762709699", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762709699", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762709699", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762709699", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762709699#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762709699", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762709699", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "WSRASVPFSAWEVEVQMRVT", "down_seq": "LGRRGAQGMAVWYTRGRGHV", "snv": [ { "evidence": [ { "id": "rs762709699", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762709699" }, { "id": "rs762709699", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762709699" }, { "id": "rs762709699", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762709699#frequency_tab" }, { "id": "rs762709699", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762709699" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816282", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G101", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs374569087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374569087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374569087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374569087", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374569087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374569087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374569087", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374569087", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SRASVPFSAWEVEVQMRVTG", "down_seq": "GRRGAQGMAVWYTRGRGHVG", "snv": [ { "evidence": [ { "id": "rs374569087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374569087" }, { "id": "rs374569087", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374569087" }, { "id": "rs374569087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374569087#frequency_tab" }, { "id": "rs374569087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374569087" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816286", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L102", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RASVPFSAWEVEVQMRVTGL", "down_seq": "RRGAQGMAVWYTRGRGHVGS", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816288", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G103", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1400291704", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400291704", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1400291704", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400291704", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1400291704", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1400291704", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs751543706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751543706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751543706", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751543706", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ASVPFSAWEVEVQMRVTGLG", "down_seq": "RGAQGMAVWYTRGRGHVGSV", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs1400291704", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400291704" }, { "id": "rs1400291704", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400291704" }, { "id": "rs1400291704", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1400291704" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816291", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R104", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs751543706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706" }, { "id": "rs751543706", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706" }, { "id": "rs751543706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751543706" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816292", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R104", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs751543706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706" }, { "id": "rs751543706", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751543706" }, { "id": "rs751543706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751543706" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816292", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1271032445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271032445", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1271032445", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271032445#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1271032445", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271032445", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1447705977", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1447705977", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1447705977", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1447705977", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VPFSAWEVEVQMRVTGLGRR", "down_seq": "AQGMAVWYTRGRGHVGSVLG", "snv": [ { "evidence": [ { "id": "rs1271032445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1271032445" }, { "id": "rs1271032445", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1271032445#frequency_tab" }, { "id": "rs1271032445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1271032445" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816298", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G106", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1447705977", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1447705977" }, { "id": "rs1447705977", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1447705977" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816297", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767697619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767697619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767697619", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767697619#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767697619", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767697619", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1216937010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216937010", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1216937010", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216937010", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PFSAWEVEVQMRVTGLGRRG", "down_seq": "QGMAVWYTRGRGHVGSVLGG", "snv": [ { "evidence": [ { "id": "rs767697619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767697619#frequency_tab" }, { "id": "rs767697619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767697619" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816300", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767697619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767697619#frequency_tab" }, { "id": "rs767697619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767697619" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816300", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767697619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767697619" }, { "id": "rs767697619", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767697619#frequency_tab" }, { "id": "rs767697619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767697619" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816300", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1216937010", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216937010" }, { "id": "rs1216937010", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216937010" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816301", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A107", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750469395", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750469395", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750469395", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750469395", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750469395", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750469395#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750469395", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750469395", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "FSAWEVEVQMRVTGLGRRGA", "down_seq": "GMAVWYTRGRGHVGSVLGGL", "snv": [ { "evidence": [ { "id": "rs750469395", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750469395" }, { "id": "rs750469395", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750469395" }, { "id": "rs750469395", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750469395#frequency_tab" }, { "id": "rs750469395", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750469395" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816305", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.109.109", "start_pos": 109, "end_pos": 109, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1324289398", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324289398", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324289398", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324289398", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SAWEVEVQMRVTGLGRRGAQ", "down_seq": "MAVWYTRGRGHVGSVLGGLA", "snv": [ { "evidence": [ { "id": "rs1324289398", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324289398" }, { "id": "rs1324289398", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324289398" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816307", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G109", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs929832365", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs929832365", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs929832365", "url": "https://www.ncbi.nlm.nih.gov/snp/rs929832365#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs929832365", "url": "http://gnomad.broadinstitute.org/awesome?query=rs929832365", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs144264457", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144264457", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs144264457", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144264457", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs144264457", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144264457#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs144264457", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144264457", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MPAVSGPGP", "down_seq": "FCLLLLLLDPHSPETGCPPL", "snv": [ { "evidence": [ { "id": "rs929832365", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs929832365" }, { "id": "rs929832365", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs929832365#frequency_tab" }, { "id": "rs929832365", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs929832365" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74812884", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L10", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs144264457", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144264457" }, { "id": "rs144264457", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs144264457" }, { "id": "rs144264457", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs144264457#frequency_tab" }, { "id": "rs144264457", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs144264457" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74812883", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.29.29", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs963855113", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs963855113", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs963855113", "url": "https://www.ensembl.org/id/rs963855113", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AWEVEVQMRVTGLGRRGAQG", "down_seq": "AVWYTRGRGHVGSVLGGLAS", "snv": [ { "evidence": [ { "id": "rs963855113", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs963855113" }, { "id": "rs963855113", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs963855113" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816311", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs563585989", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563585989", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1054149963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1054149963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1054149963", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1054149963#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1054149963", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1054149963", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "WEVEVQMRVTGLGRRGAQGM", "down_seq": "VWYTRGRGHVGSVLGGLASW", "snv": [ { "evidence": [ { "id": "rs563585989", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563585989" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "=", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816429", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.0002", "site_lbl": "A111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1054149963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1054149963" }, { "id": "rs1054149963", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1054149963#frequency_tab" }, { "id": "rs1054149963", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1054149963" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816428", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816428", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A111", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.91.91", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376132416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376132416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376132416", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376132416#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376132416", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376132416", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EVEVQMRVTGLGRRGAQGMA", "down_seq": "WYTRGRGHVGSVLGGLASWD", "snv": [ { "evidence": [ { "id": "rs376132416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416" }, { "id": "rs376132416", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416" }, { "id": "rs376132416", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376132416#frequency_tab" }, { "id": "rs376132416", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376132416" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816430", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V112", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376132416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416" }, { "id": "rs376132416", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376132416" }, { "id": "rs376132416", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376132416#frequency_tab" }, { "id": "rs376132416", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376132416" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816430", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V112", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs993169993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs993169993", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs993169993", "url": "https://www.ncbi.nlm.nih.gov/snp/rs993169993#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs993169993", "url": "http://gnomad.broadinstitute.org/awesome?query=rs993169993", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "VEVQMRVTGLGRRGAQGMAV", "down_seq": "YTRGRGHVGSVLGGLASWDG", "snv": [ { "evidence": [ { "id": "rs993169993", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs993169993" }, { "id": "rs993169993", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs993169993#frequency_tab" }, { "id": "rs993169993", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs993169993" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816434", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2081390930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2081390930", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2081390930", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2081390930#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EVQMRVTGLGRRGAQGMAVW", "down_seq": "TRGRGHVGSVLGGLASWDGI", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816438", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Y114", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816437", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y114", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2081390930", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2081390930" }, { "id": "rs2081390930", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2081390930#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816436", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y114", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs899576101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs899576101", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs899576101", "url": "https://www.ensembl.org/id/rs899576101", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2063890870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063890870", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2063890870", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063890870#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VQMRVTGLGRRGAQGMAVWY", "down_seq": "RGRGHVGSVLGGLASWDGIG", "snv": [ { "evidence": [ { "id": "rs899576101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs899576101" }, { "id": "rs899576101", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs899576101" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816440", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2063890870", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063890870" }, { "id": "rs2063890870", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063890870#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816439", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1366395705", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1366395705", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1366395705", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1366395705", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1366395705", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1366395705", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs758984056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758984056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758984056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758984056", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758984056", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758984056#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758984056", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758984056", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QMRVTGLGRRGAQGMAVWYT", "down_seq": "GRGHVGSVLGGLASWDGIGI", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816443", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R116", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" }, { "id": "rs1366395705", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1366395705" }, { "id": "rs1366395705", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1366395705" }, { "id": "rs1366395705", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1366395705" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816443", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R116", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs758984056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758984056" }, { "id": "rs758984056", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758984056" }, { "id": "rs758984056", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758984056#frequency_tab" }, { "id": "rs758984056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758984056" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816442", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778115839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778115839", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778115839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778115839", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778115839", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778115839", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MRVTGLGRRGAQGMAVWYTR", "down_seq": "RGHVGSVLGGLASWDGIGIF", "snv": [ { "evidence": [ { "id": "rs778115839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778115839" }, { "id": "rs778115839", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778115839" }, { "id": "rs778115839", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778115839" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816446", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G117", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2063890965", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063890965", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2063890965", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063890965#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RVTGLGRRGAQGMAVWYTRG", "down_seq": "GHVGSVLGGLASWDGIGIFF", "snv": [ { "evidence": [ { "id": "rs2063890965", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2063890965" }, { "id": "rs2063890965", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2063890965#frequency_tab" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816448", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R118", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1029416875", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1029416875", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1029416875", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1029416875#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1337065501", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337065501", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1337065501", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337065501#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1337065501", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337065501", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VTGLGRRGAQGMAVWYTRGR", "down_seq": "HVGSVLGGLASWDGIGIFFD", "snv": [ { "evidence": [ { "id": "rs1029416875", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1029416875" }, { "id": "rs1029416875", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1029416875#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816451", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G119", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1337065501", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1337065501" }, { "id": "rs1337065501", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1337065501#frequency_tab" }, { "id": "rs1337065501", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1337065501" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816452", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G119", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.139.139", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs562811750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562811750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs562811750", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs562811750", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs562811750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562811750", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs562811750", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562811750#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs562811750", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562811750", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MPAVSGPGPL", "down_seq": "CLLLLLLDPHSPETGCPPLR", "snv": [ { "evidence": [ { "id": "rs562811750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562811750" }, { "id": "rs562811750", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs562811750" }, { "id": "rs562811750", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs562811750" }, { "id": "rs562811750", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs562811750#frequency_tab" }, { "id": "rs562811750", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs562811750" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74812886", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "F11", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.7.7", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9HAT1-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9HAT1-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9HAT1-1.25.25", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9HAT1-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.31.31", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9HAT1-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "Q9HAT1-1", "length": 526, "uniprot_id": "LMA1L_HUMAN", "protein_name": "Protein ERGIC-53-like", "refseq_ac": "NP_068591", "refseq_name": "protein ERGIC-53-like precursor", "gene_name": "LMAN1L", "gene_names_uniprotkb": "LMAN1L; ERGL; PRO7174", "gene_names_refseq": "ERGIC-53L; ERGL; LMAN1L", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9HAT1", "url": "https://www.uniprot.org/uniprotkb/Q9HAT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9HAT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs747461294", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747461294", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747461294", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747461294", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747461294", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747461294", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "TGLGRRGAQGMAVWYTRGRG", "down_seq": "VGSVLGGLASWDGIGIFFDS", "snv": [ { "evidence": [ { "id": "Q9HAT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9HAT1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, lectin/l-type).", "chr_id": "15", "chr_pos": "74816455", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H120", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs747461294", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747461294" }, { "id": "rs747461294", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747461294" }, { "id": "rs747461294", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747461294" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, lectin/l-type.", "chr_id": "15", "chr_pos": "74816454", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H120", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "75", "end_pos": "75" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "109", "end_pos": "109" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "189", "end_pos": "189" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "245", "end_pos": "245" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "254", "end_pos": "254" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "310", "end_pos": "310" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "329", "end_pos": "329" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "348", "end_pos": "348" }, { "start_pos": "349", "end_pos": "349" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "364", "end_pos": "364" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "383", "end_pos": "383" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "422", "end_pos": "422" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "428", "end_pos": "428" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "451", "end_pos": "451" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "461", "end_pos": "461" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "468", "end_pos": "468" }, { "start_pos": "470", "end_pos": "470" }, { "start_pos": "472", "end_pos": "472" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "481", "end_pos": "481" }, { "start_pos": "482", "end_pos": "482" }, { "start_pos": "486", "end_pos": "486" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "491", "end_pos": "491" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "513", "end_pos": "513" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "521", "end_pos": "521" }, { "start_pos": "523", "end_pos": "523" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "525", "end_pos": "525" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "79", "end_pos": "79" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "91", "end_pos": "91" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9HAT1-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9HAT1-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9HAT1-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q9HAT1-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q9HAT1-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q9HAT1-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9HAT1-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q9HAT1-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9HAT1-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q9HAT1-1.109.109", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9HAT1-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9HAT1-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9HAT1-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9HAT1-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9HAT1-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9HAT1-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9HAT1-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9HAT1-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9HAT1-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q9HAT1-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9HAT1-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9HAT1-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9HAT1-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9HAT1-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9HAT1-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9HAT1-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9HAT1-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9HAT1-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9HAT1-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9HAT1-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q9HAT1-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q9HAT1-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9HAT1-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9HAT1-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9HAT1-1.139.139", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9HAT1-1.140.140", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] } ]